python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/SingleMoleculeCorrelation-NMI-matrix-C-BAM.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa DNase-ENCFF759OLD.2kbp.split0 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split10 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split11 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split12 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split13 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split14 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split15 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split16 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split17 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split18 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split19 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split1999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split20 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split21 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split22 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split23 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split24 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split25 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split26 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split27 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split28 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split29 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split2999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split30 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split31 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split32 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split33 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split34 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split35 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split36 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split37 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split38 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split39 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split3999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split40 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split41 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split42 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split43 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split44 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split45 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split46 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split47 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split48 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split49 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split4999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split50 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split51 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split52 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split53 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split54 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split55 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split56 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split57 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split58 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split59 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split5999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split60 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split61 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split62 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split63 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split64 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split65 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split66 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split67 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split68 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split69 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split6999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split70 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split71 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split72 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split73 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7377 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7378 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7379 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7380 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7381 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7382 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7383 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7384 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7385 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7386 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7387 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7388 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7389 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7390 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7391 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7392 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7393 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7394 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7395 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7396 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7397 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7398 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7399 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split74 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7400 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7401 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7402 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7403 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7404 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7405 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7406 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7407 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7408 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7409 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7410 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7411 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7412 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7413 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7414 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7415 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7416 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7417 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7418 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7419 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7420 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7421 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7422 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7423 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7424 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7425 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7426 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7427 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7428 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7429 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7430 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7431 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7432 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7433 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7434 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7435 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7436 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7437 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7438 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7439 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7440 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7441 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7442 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7443 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7444 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7445 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7446 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7447 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7448 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7449 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7450 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7451 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7452 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7453 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7454 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7455 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7456 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7457 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7458 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7459 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7460 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7461 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7462 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7463 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7464 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7465 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7466 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7467 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7468 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7469 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7470 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7471 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7472 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7473 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7474 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7475 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7476 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7477 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7478 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7479 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7480 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7481 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7482 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7483 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7484 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7485 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7486 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7487 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7488 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7489 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7490 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7491 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7492 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7493 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7494 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7495 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7496 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7497 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7498 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7499 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split75 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7500 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7501 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7502 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7503 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7504 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7505 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7506 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7507 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7508 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7509 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7510 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7511 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7512 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7513 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7514 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7515 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7516 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7517 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7518 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7519 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7520 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7521 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7522 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7523 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7524 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7525 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7526 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7527 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7528 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7529 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7530 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7531 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7532 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7533 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7534 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7535 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7536 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7537 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7538 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7539 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7540 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7541 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7542 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7543 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7544 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7545 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7546 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7547 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7548 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7549 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7550 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7551 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7552 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7553 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7554 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7555 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7556 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7557 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7558 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7559 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7560 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7561 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7562 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7563 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7564 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7565 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7566 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7567 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7568 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7569 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7570 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7571 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7572 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7573 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7574 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7575 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7576 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7577 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7578 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7579 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7580 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7581 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7582 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7583 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7584 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7585 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7586 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7587 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7588 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7589 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7590 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7591 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7592 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7593 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7594 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7595 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7596 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7597 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7598 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7599 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split76 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7600 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7601 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7602 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7603 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7604 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7605 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7606 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7607 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7608 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7609 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7610 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7611 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7612 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7613 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7614 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7615 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7616 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7617 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7618 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7619 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7620 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7621 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7622 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7623 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7624 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7625 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7626 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7627 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7628 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7629 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7630 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7631 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7632 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7633 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7634 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7635 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7636 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7637 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7638 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7639 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7640 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7641 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7642 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7643 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7644 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7645 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7646 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7647 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7648 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7649 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7650 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7651 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7652 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7653 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7654 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7655 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7656 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7657 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7658 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7659 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7660 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7661 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7662 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7663 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7664 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7665 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7666 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7667 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7668 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7669 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7670 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7671 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7672 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7673 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7674 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7675 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7676 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7677 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7678 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7679 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7680 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7681 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7682 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7683 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7684 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7685 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7686 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7687 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7688 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7689 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7690 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7691 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7692 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7693 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7694 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7695 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7696 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7697 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7698 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7699 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split77 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7700 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7701 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7702 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7703 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7704 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7705 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7706 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7707 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7708 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7709 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7710 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7711 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7712 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7713 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7714 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7715 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7716 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7717 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7718 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7719 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7720 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7721 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7722 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7723 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7724 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7725 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7726 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7727 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7728 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7729 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7730 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7731 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7732 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7733 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7734 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7735 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7736 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7737 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7738 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7739 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7740 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7741 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7742 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7743 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7744 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7745 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7746 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7747 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7748 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7749 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7750 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7751 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7752 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7753 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7754 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7755 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7756 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7757 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7758 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7759 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7760 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7761 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7762 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7763 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7764 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7765 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7766 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7767 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7768 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7769 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7770 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7771 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7772 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7773 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7774 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7775 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7776 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7777 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split778 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split779 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split78 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split780 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split781 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split782 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split783 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split784 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split785 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split786 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split787 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split788 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split789 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split79 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split790 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split791 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split792 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split793 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split794 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split795 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split796 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split797 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split798 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split799 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split7999 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split80 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split800 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8000 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8001 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8002 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8003 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8004 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8005 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8006 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8007 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8008 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8009 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split801 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8010 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8011 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8012 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8013 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8014 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8015 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8016 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8017 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8018 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8019 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split802 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8020 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8021 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8022 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8023 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8024 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8025 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8026 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8027 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8028 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8029 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split803 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8030 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8031 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8032 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8033 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8034 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8035 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8036 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8037 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8038 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8039 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split804 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8040 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8041 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8042 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8043 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8044 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8045 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8046 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8047 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8048 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8049 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split805 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8050 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8051 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8052 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8053 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8054 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8055 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8056 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8057 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8058 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8059 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split806 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8060 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8061 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8062 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8063 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8064 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8065 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8066 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8067 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8068 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8069 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split807 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8070 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8071 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8072 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8073 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8074 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8075 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8076 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8077 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8078 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8079 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split808 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8080 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8081 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8082 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8083 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8084 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8085 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8086 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8087 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8088 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8089 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split809 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8090 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8091 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8092 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8093 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8094 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8095 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8096 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8097 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8098 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8099 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split81 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split810 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8100 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8101 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8102 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8103 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8104 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8105 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8106 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8107 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8108 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8109 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split811 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8110 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8111 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8112 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8113 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8114 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8115 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8116 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8117 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8118 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8119 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split812 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8120 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8121 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8122 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8123 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8124 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8125 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8126 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8127 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8128 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8129 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split813 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8130 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8131 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8132 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8133 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8134 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8135 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8136 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8137 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8138 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8139 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split814 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8140 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8141 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8142 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8143 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8144 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8145 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8146 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8147 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8148 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8149 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split815 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8150 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8151 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8152 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8153 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8154 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8155 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8156 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8157 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8158 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8159 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split816 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8160 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8161 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8162 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8163 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8164 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8165 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8166 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8167 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8168 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8169 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split817 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8170 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8171 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8172 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8173 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8174 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8175 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8176 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8177 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8178 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8179 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split818 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8180 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8181 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8182 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8183 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8184 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8185 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8186 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8187 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8188 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8189 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split819 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8190 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8191 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8192 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8193 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8194 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8195 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8196 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8197 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8198 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8199 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split82 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split820 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8200 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8201 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8202 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8203 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8204 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8205 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8206 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8207 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8208 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8209 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split821 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8210 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8211 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8212 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8213 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8214 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8215 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8216 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8217 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8218 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8219 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split822 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8220 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8221 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8222 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8223 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8224 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8225 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8226 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8227 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8228 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8229 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split823 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8230 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8231 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8232 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8233 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8234 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8235 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8236 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8237 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8238 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8239 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split824 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8240 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8241 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8242 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8243 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8244 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8245 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8246 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8247 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8248 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8249 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split825 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8250 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8251 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8252 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8253 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8254 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8255 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8256 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8257 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8258 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8259 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split826 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8260 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8261 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8262 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8263 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8264 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8265 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8266 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8267 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8268 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8269 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split827 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8270 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8271 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8272 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8273 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8274 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8275 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8276 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8277 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8278 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8279 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split828 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8280 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8281 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8282 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8283 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8284 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8285 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8286 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8287 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8288 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8289 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split829 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8290 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8291 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8292 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8293 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8294 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8295 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8296 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8297 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8298 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8299 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split83 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split830 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8300 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8301 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8302 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8303 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8304 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8305 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8306 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8307 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8308 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8309 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split831 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8310 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8311 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8312 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8313 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8314 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8315 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8316 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8317 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8318 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8319 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split832 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8320 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8321 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8322 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8323 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8324 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8325 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8326 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8327 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8328 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8329 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split833 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8330 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8331 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8332 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8333 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8334 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8335 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8336 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8337 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8338 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8339 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split834 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8340 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8341 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8342 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8343 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8344 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8345 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8346 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8347 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8348 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8349 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split835 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8350 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8351 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8352 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8353 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8354 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8355 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8356 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8357 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8358 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8359 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split836 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8360 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8361 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8362 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8363 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8364 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8365 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8366 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8367 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8368 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8369 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split837 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8370 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8371 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8372 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8373 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8374 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8375 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split8376 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split838 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split839 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split84 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split840 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split841 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split842 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split843 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split844 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split845 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split846 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split847 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split848 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split849 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split85 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split850 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split851 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split852 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split853 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split854 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split855 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split856 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split857 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split858 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split859 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split86 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split860 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split861 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split862 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split863 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split864 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split865 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split866 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split867 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split868 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split869 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split87 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split870 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split871 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split872 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split873 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split874 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split875 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split876 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split877 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split878 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split879 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split88 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split880 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split881 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split882 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split883 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split884 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split885 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split886 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split887 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split888 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split889 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split89 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split890 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split891 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split892 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split893 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split894 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split895 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split896 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split897 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split898 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split899 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split9 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split90 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split900 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split901 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split902 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split903 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split904 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split905 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split906 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split907 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split908 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split909 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split91 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split910 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split911 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split912 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split913 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split914 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split915 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split916 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split917 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split918 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split919 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split92 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split920 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split921 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split922 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split923 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split924 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split925 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split926 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split927 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split928 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split929 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split93 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split930 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split931 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split932 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split933 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split934 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split935 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split936 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split937 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split938 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split939 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split94 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split940 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split941 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split942 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split943 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split944 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split945 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split946 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split947 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split948 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split949 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split95 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split950 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split951 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split952 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split953 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split954 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split955 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split956 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split957 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split958 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split959 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split96 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split960 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split961 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split962 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split963 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split964 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split965 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split966 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split967 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split968 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split969 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split97 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split970 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split971 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split972 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split973 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split974 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split975 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split976 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split977 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split978 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split979 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split98 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split980 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split981 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split982 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split983 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split984 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split985 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split986 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split987 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split988 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split989 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split99 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split990 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split991 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split992 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split993 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split994 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split995 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split996 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split997 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split998 0 1 2 50 DNase-ENCFF759OLD.2kbp.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 DNase-ENCFF759OLD.2kbp.split999 0 1 2 50 DNase-ENCFF759OLD.2kbp.split999.NMI