python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.gtf hen2-4_pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/TAIR10.chrom.sizes  sam_reads_in_genes-hen2-4_pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.gtf rrp4-2_pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/TAIR10.chrom.sizes  sam_reads_in_genes-rrp4-2_pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/Arabidopsis_thaliana.TAIR10.19.fixed.gtf wt_pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/TAIR10/TAIR10.chrom.sizes  sam_reads_in_genes-wt_pooled -nomulti