python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.gtf RAMPAGE_IRBB7_Control-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes  sam_reads_in_genes-RAMPAGE_IRBB7_Control -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.gtf RAMPAGE_IRBB7_Treated-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes  sam_reads_in_genes-RAMPAGE_IRBB7_Treated -nomulti