python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T106_b13_Eye_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T180_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T186_b13_Eye_PCW23.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T410_b13_Eye_PCW13.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T51_b13_Eye_PCW20.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T5_b13_Eye_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL182_b13_ATAC_EyeRedo.T79_b13_Eye_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T107_b12_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T132_b12_lung_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T164_b12_Lung_PCW10.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T226_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T256_b12_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T286_b12_Lung_PCW14.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T304_b12_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL159_b12_ATAC_LungRedo.T408L_b12_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T238_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T269_b10_Stomach_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T303_b10_Esophagus_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T322_b10_Stomach_PCW21.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T35_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T399_b10_Stomach_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL122_b10_ATAC_StomachEsophagus.T53_b10_Stomach_PCW20.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T109_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T11_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T178_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T187_b14_Skin_PCW23.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T408S_b14_Skin_PCW19.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T45_b14_Skin_PCW17.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T60_b14_Skin_PCW20.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg20/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 SL187_b14_ATAC_Skin.T85_b14_Skin_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats