python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_genomic.gtf HARMI-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_genomic.chrom.sizes  sam_reads_in_genes-HARMI-1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_genomic.gtf HARMI-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Helicoverpa_armigera-Harm_1.0/GCA_002156985.1_Harm_1.0_genomic.chrom.sizes  sam_reads_in_genes-HARMI-2 -nomulti