python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Acyrthosiphon_pisum/Acyrthosiphon_pisum.GCA_000142985.2.20.gtf APISU-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Acyrthosiphon_pisum/Acyrthosiphon_pisum.GCA_000142985.2.20.chrom.sizes  sam_reads_in_genes-APISU-1 -nomulti