python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Laodelphax_striatellus-ASM333518v2/GCA_003335185.2_ASM333518v2_genomic.gtf LSTRI-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Laodelphax_striatellus-ASM333518v2/GCA_003335185.2_ASM333518v2_genomic.chrom.sizes  sam_reads_in_genes-LSTRI-1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Laodelphax_striatellus-ASM333518v2/GCA_003335185.2_ASM333518v2_genomic.gtf LSTRI-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Insects/Laodelphax_striatellus-ASM333518v2/GCA_003335185.2_ASM333518v2_genomic.chrom.sizes  sam_reads_in_genes-LSTRI-2 -nomulti