python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5_genomic.gtf Chlamydomonas_reinhardtii_liquid_culture_5GRO-seq-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.chrom.sizes  sam_reads_in_genes-Chlamydomonas_reinhardtii_liquid_culture_5GRO-seq-pooled -nomulti
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/SAM_reads_in_genes3_BAM.py /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5_genomic.gtf Chlamydomonas_reinhardtii_liquid_culture_GRO-seq_r1-GSM7439228-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.chrom.sizes  sam_reads_in_genes-Chlamydomonas_reinhardtii_liquid_culture_GRO-seq_r1-GSM7439228 -nomulti