python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split0 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split1 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split10 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split100 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split101 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split102 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split103 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split104 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split105 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split106 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split107 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split108 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split109 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split11 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split110 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split111 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split112 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split113 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split114 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split115 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split116 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split117 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split118 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split119 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split12 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split120 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split121 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split122 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split123 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split124 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split125 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split126 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split127 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split128 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split129 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split13 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split130 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split131 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split132 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split133 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split134 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split135 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split136 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split137 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split138 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split139 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split14 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split140 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split141 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split142 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split143 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split144 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split145 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split146 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split147 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split148 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split149 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split15 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split150 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split151 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split152 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split153 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split154 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split155 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split156 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split157 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split158 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split159 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split16 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split160 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split161 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split162 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split163 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split164 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split165 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split166 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split167 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split168 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split169 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split17 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split170 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split171 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split172 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split173 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split174 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split175 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split176 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split177 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split178 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split179 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split18 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split180 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split181 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split182 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split183 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split184 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split185 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split186 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split187 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split188 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split189 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split19 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split190 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split191 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split192 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split193 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split194 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split195 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split196 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split197 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split198 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split199 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split2 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split20 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split200 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split201 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split202 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split203 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split204 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split205 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split206 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split207 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split208 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split209 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split21 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split210 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split211 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split212 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split213 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split214 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split215 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split216 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split217 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split218 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split219 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split22 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split220 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split221 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split222 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split223 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split224 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split225 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split226 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split227 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split228 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split229 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split23 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split230 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split231 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split232 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split233 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split234 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split235 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split236 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split237 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split238 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split239 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split24 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split240 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split241 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split242 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split243 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split244 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split245 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split246 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split247 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split248 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split249 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split25 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split250 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split251 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split252 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split253 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split254 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split255 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split256 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split257 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split258 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split259 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split26 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split260 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split261 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split262 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split263 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split264 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split265 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split266 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split267 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split268 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split269 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split27 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split270 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split271 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split272 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split273 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split274 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split275 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split276 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split277 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split278 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split279 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split28 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split280 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split281 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split282 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split283 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split284 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split285 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split286 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split287 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split288 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split289 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split29 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split290 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split291 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split292 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split293 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split294 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split295 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split296 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split297 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split298 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split299 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split3 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split30 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split300 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split301 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split302 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split303 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split304 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split305 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split306 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split307 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split308 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split309 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split31 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split310 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split311 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split312 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split313 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split314 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split315 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split316 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split317 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split318 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split319 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split32 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split320 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split321 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split322 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split323 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split324 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split325 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split326 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split327 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split328 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split329 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split33 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split330 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split331 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split332 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split34 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split35 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split36 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split37 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split38 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split39 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split4 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split40 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split41 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split42 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split43 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split44 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split45 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split46 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split47 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split48 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split49 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split5 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split50 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split51 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split52 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split53 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split54 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split55 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split56 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split57 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split58 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split59 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split6 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split60 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split61 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split62 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split63 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split64 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split65 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split66 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split67 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split68 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split69 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split7 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split70 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split71 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split72 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split73 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split74 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split75 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split76 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split77 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split78 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split79 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split8 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split80 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split81 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split82 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split83 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split84 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split85 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split86 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split87 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split88 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split89 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split9 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split90 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split91 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split92 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split93 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split94 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split95 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split96 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split97 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split98 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded
python /oak/stanford/groups/akundaje/marinovg/code/bisulfite/dSMF-footprints.py /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress/L3449-L3413-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress/L3450-L3414-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress/L3451-L3416-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress/L3452-L3417-GM18278_200K_15uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress/L3453-L3419-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress/L3454-L3420-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress/L3455-L3422-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam,/oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-PBAT-NOME_dSMF/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress/L3456-L3423-GM18278_200K_10uL_CseDa01_PUREexpress.415630.trimmed.bwameth.hg38.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/chrM.fa C chrM-tiling.bed.split99 0 1 2 2 chrM-tiling.250bp-SMF-plots -heatmap ~/code/plotting/heatmap.py 10 10 binary 10,100 -minCov 1 -unstranded