python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py TCAST-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-TCAST-1 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20+chrM.chrom.sizes  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py TCAST-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-TCAST-2 -bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20+chrM.chrom.sizes  samtools -paired