python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 170858.ATAC.trimmed.hg38.unique.nochrM.hg38.BC_dedup.bam SAMstats-170858.ATAC.trimmed.hg38.unique.nochrM.hg38.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 -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py 170858.ATAC.trimmed.hg38.BWA.unique.nochrM.hg38.BC_dedup.bam SAMstats-170858.ATAC.trimmed.hg38.BWA.unique.nochrM.hg38.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 -uniqueBAM &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py 170858.ATAC.trimmed.hg38.unique.nochrM.hg38.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 170858.ATAC.trimmed.hg38.unique.nochrM.hg38.BC_dedup.per_cell_stats &
python /oak/stanford/groups/akundaje/marinovg/code/single-cell-RNA-seq/SHARE-seq_ATAC_stats_per_cell.py 170858.ATAC.trimmed.hg38.BWA.unique.nochrM.hg38.BC_dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg38/2016-11-16-refFlat.TSS-0bp.bed 0 1 2000 200 170858.ATAC.trimmed.hg38.BWA.unique.nochrM.hg38.BC_dedup.per_cell_stats &