python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Oxytricha_trifallax_asm_v1.1/GCA_000295675.1_oxytricha_asm_v1.1_genomic.gtf Oxy_TSSseq-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Oxytricha_trifallax_asm_v1.1/GCA_000295675.1_oxytricha_asm_v1.1_genomic.chrom.sizes  sam_reads_in_genes-Oxy_TSSseq-pooled -nomulti