python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/2019-02-06-PomBase.fixed.gtf fft2fft3-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes  sam_reads_in_genes-fft2fft3-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/2019-02-06-PomBase.fixed.gtf wt-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes  sam_reads_in_genes-wt-pooled -nomulti