python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SK-L234-HeartPCW18_FT005_ATAC5k_2.2x30mers.hg38-male.unique.BC_dedup.bam SAMstats-SK-L234-HeartPCW18_FT005_ATAC5k_2.2x30mers.hg38-male.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SK-L233-HeartPCW18_FT005_ATAC5k_1.2x30mers.hg38-male.unique.BC_dedup.bam SAMstats-SK-L233-HeartPCW18_FT005_ATAC5k_1.2x30mers.hg38-male.unique.BC_dedup -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SK-L234-HeartPCW18_FT005_ATAC5k_2.2x30mers.hg38-male.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 SK-L234-HeartPCW18_FT005_ATAC5k_2.2x30mers.hg38-male.unique.BC_dedup.per_cell_stats &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py SK-L233-HeartPCW18_FT005_ATAC5k_1.2x30mers.hg38-male.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 SK-L233-HeartPCW18_FT005_ATAC5k_1.2x30mers.hg38-male.unique.BC_dedup.per_cell_stats &