python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Aspergillus_luchuensis-AspL_2604/GCA_001602395.1_AspL_2604_genomic.gtf Ctrl_pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Aspergillus_luchuensis-AspL_2604/GCA_001602395.1_AspL_2604_genomic.chrom.sizes  sam_reads_in_genes-Ctrl_pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Aspergillus_luchuensis-AspL_2604/GCA_001602395.1_AspL_2604_genomic.gtf sirD_pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Aspergillus_luchuensis-AspL_2604/GCA_001602395.1_AspL_2604_genomic.chrom.sizes  sam_reads_in_genes-sirD_pooled -nomulti