python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py primary_keratinocyte-d30.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam SAMstats-primary_keratinocyte-d30.b2.RAMPAGE -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam SAMstats-primary_keratinocyte-d25.b1.RAMPAGE -bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.19/samtools -paired