python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.gtf Selaginella_moellendorffii_stem_leaves_5GRO-seq_r1-GSM7439248-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.chrom.sizes  sam_reads_in_genes-Selaginella_moellendorffii_stem_leaves_5GRO-seq_r1-GSM7439248 -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.gtf Selaginella_moellendorffii_stem_leaves_GRO-seq_r1-GSM7439251-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Selaginella_moellendorffii/Selaginella_moellendorffii.v1.0.19.chrom.sizes  sam_reads_in_genes-Selaginella_moellendorffii_stem_leaves_GRO-seq_r1-GSM7439251 -nomulti