python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL283_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T175_b18_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 SL283_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T198_b18_Lung_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 SL283_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T24_b18_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 SL283_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T305_b18_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 SL283_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T333_b18_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 SL283_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T49_b18_Lung_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 SL283_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL283_b18_ATAC_lungredo2.T77_b18_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 SL284_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T175_b18_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 SL284_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T198_b18_Lung_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 SL284_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T24_b18_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 SL284_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T305_b18_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 SL284_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T333_b18_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 SL284_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T49_b18_Lung_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 SL284_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL284_b18_ATAC_lungredo2.T77_b18_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/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL283_b18_ATAC_lungredo2.T175_b18_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 SL283_b18_ATAC_lungredo2.T175_b18_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 SL283_b18_ATAC_lungredo2.T198_b18_Lung_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 SL283_b18_ATAC_lungredo2.T198_b18_Lung_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 SL283_b18_ATAC_lungredo2.T24_b18_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 SL283_b18_ATAC_lungredo2.T24_b18_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 SL283_b18_ATAC_lungredo2.T305_b18_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 SL283_b18_ATAC_lungredo2.T305_b18_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 SL283_b18_ATAC_lungredo2.T333_b18_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 SL283_b18_ATAC_lungredo2.T333_b18_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 SL283_b18_ATAC_lungredo2.T49_b18_Lung_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 SL283_b18_ATAC_lungredo2.T49_b18_Lung_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 SL283_b18_ATAC_lungredo2.T77_b18_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 SL283_b18_ATAC_lungredo2.T77_b18_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 SL284_b18_ATAC_lungredo2.T175_b18_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 SL284_b18_ATAC_lungredo2.T175_b18_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 SL284_b18_ATAC_lungredo2.T198_b18_Lung_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 SL284_b18_ATAC_lungredo2.T198_b18_Lung_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 SL284_b18_ATAC_lungredo2.T24_b18_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 SL284_b18_ATAC_lungredo2.T24_b18_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 SL284_b18_ATAC_lungredo2.T305_b18_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 SL284_b18_ATAC_lungredo2.T305_b18_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 SL284_b18_ATAC_lungredo2.T333_b18_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 SL284_b18_ATAC_lungredo2.T333_b18_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 SL284_b18_ATAC_lungredo2.T49_b18_Lung_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 SL284_b18_ATAC_lungredo2.T49_b18_Lung_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 SL284_b18_ATAC_lungredo2.T77_b18_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 SL284_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL285_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T175_b18_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 SL285_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T198_b18_Lung_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 SL285_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T24_b18_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 SL285_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T305_b18_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 SL285_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T333_b18_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 SL285_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T49_b18_Lung_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 SL285_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL285_b18_ATAC_lungredo2.T77_b18_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 SL286_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T175_b18_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 SL286_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T198_b18_Lung_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 SL286_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T24_b18_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 SL286_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T305_b18_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 SL286_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T333_b18_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 SL286_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T49_b18_Lung_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 SL286_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL286_b18_ATAC_lungredo2.T77_b18_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/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL285_b18_ATAC_lungredo2.T175_b18_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 SL285_b18_ATAC_lungredo2.T175_b18_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 SL285_b18_ATAC_lungredo2.T198_b18_Lung_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 SL285_b18_ATAC_lungredo2.T198_b18_Lung_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 SL285_b18_ATAC_lungredo2.T24_b18_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 SL285_b18_ATAC_lungredo2.T24_b18_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 SL285_b18_ATAC_lungredo2.T305_b18_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 SL285_b18_ATAC_lungredo2.T305_b18_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 SL285_b18_ATAC_lungredo2.T333_b18_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 SL285_b18_ATAC_lungredo2.T333_b18_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 SL285_b18_ATAC_lungredo2.T49_b18_Lung_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 SL285_b18_ATAC_lungredo2.T49_b18_Lung_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 SL285_b18_ATAC_lungredo2.T77_b18_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 SL285_b18_ATAC_lungredo2.T77_b18_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 SL286_b18_ATAC_lungredo2.T175_b18_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 SL286_b18_ATAC_lungredo2.T175_b18_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 SL286_b18_ATAC_lungredo2.T198_b18_Lung_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 SL286_b18_ATAC_lungredo2.T198_b18_Lung_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 SL286_b18_ATAC_lungredo2.T24_b18_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 SL286_b18_ATAC_lungredo2.T24_b18_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 SL286_b18_ATAC_lungredo2.T305_b18_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 SL286_b18_ATAC_lungredo2.T305_b18_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 SL286_b18_ATAC_lungredo2.T333_b18_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 SL286_b18_ATAC_lungredo2.T333_b18_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 SL286_b18_ATAC_lungredo2.T49_b18_Lung_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 SL286_b18_ATAC_lungredo2.T49_b18_Lung_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 SL286_b18_ATAC_lungredo2.T77_b18_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 SL286_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SL288_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T175_b18_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 SL288_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T198_b18_Lung_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 SL288_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T24_b18_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 SL288_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T305_b18_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 SL288_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T333_b18_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 SL288_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T49_b18_Lung_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 SL288_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL288_b18_ATAC_lungredo2.T77_b18_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 SL287_b18_ATAC_lungredo2.T175_b18_Lung_PCW19.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T175_b18_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 SL287_b18_ATAC_lungredo2.T198_b18_Lung_PCW23.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T198_b18_Lung_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 SL287_b18_ATAC_lungredo2.T24_b18_Lung_PCW17.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T24_b18_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 SL287_b18_ATAC_lungredo2.T305_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T305_b18_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 SL287_b18_ATAC_lungredo2.T333_b18_Lung_PCW21.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T333_b18_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 SL287_b18_ATAC_lungredo2.T49_b18_Lung_PCW20.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T49_b18_Lung_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 SL287_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.bam SAMstats-SL287_b18_ATAC_lungredo2.T77_b18_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/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SL288_b18_ATAC_lungredo2.T175_b18_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 SL288_b18_ATAC_lungredo2.T175_b18_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 SL288_b18_ATAC_lungredo2.T198_b18_Lung_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 SL288_b18_ATAC_lungredo2.T198_b18_Lung_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 SL288_b18_ATAC_lungredo2.T24_b18_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 SL288_b18_ATAC_lungredo2.T24_b18_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 SL288_b18_ATAC_lungredo2.T305_b18_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 SL288_b18_ATAC_lungredo2.T305_b18_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 SL288_b18_ATAC_lungredo2.T333_b18_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 SL288_b18_ATAC_lungredo2.T333_b18_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 SL288_b18_ATAC_lungredo2.T49_b18_Lung_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 SL288_b18_ATAC_lungredo2.T49_b18_Lung_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 SL288_b18_ATAC_lungredo2.T77_b18_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 SL288_b18_ATAC_lungredo2.T77_b18_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 SL287_b18_ATAC_lungredo2.T175_b18_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 SL287_b18_ATAC_lungredo2.T175_b18_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 SL287_b18_ATAC_lungredo2.T198_b18_Lung_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 SL287_b18_ATAC_lungredo2.T198_b18_Lung_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 SL287_b18_ATAC_lungredo2.T24_b18_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 SL287_b18_ATAC_lungredo2.T24_b18_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 SL287_b18_ATAC_lungredo2.T305_b18_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 SL287_b18_ATAC_lungredo2.T305_b18_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 SL287_b18_ATAC_lungredo2.T333_b18_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 SL287_b18_ATAC_lungredo2.T333_b18_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 SL287_b18_ATAC_lungredo2.T49_b18_Lung_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 SL287_b18_ATAC_lungredo2.T49_b18_Lung_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 SL287_b18_ATAC_lungredo2.T77_b18_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 SL287_b18_ATAC_lungredo2.T77_b18_Lung_PCW18.2x36mers.hg38.unique.BC_dedup.per_cell_stats