python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Chelicerata/Tetranychus_urticae/Tetranychus_urticae.GCA_000239435.1.20.gtf TURTI-1-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Chelicerata/Tetranychus_urticae/Tetranychus_urticae.GCA_000239435.1.20.chrom.sizes  sam_reads_in_genes-TURTI-1 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Chelicerata/Tetranychus_urticae/Tetranychus_urticae.GCA_000239435.1.20.gtf TURTI-2-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Metazoa/Chelicerata/Tetranychus_urticae/Tetranychus_urticae.GCA_000239435.1.20.chrom.sizes  sam_reads_in_genes-TURTI-2 -nomulti