python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20.gtf TCAST-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20+chrM.chrom.sizes  sam_reads_in_genes-TCAST-1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20.gtf TCAST-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Tribolium_castaneum/Tribolium_castaneum.Tcas3.20+chrM.chrom.sizes  sam_reads_in_genes-TCAST-2 -nomulti