python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_IRBB7_Control-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RAMPAGE_IRBB7_Control -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py RAMPAGE_IRBB7_Treated-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-RAMPAGE_IRBB7_Treated -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes  samtools -paired