python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Chlamydomonas_reinhardtii_liquid_culture_5GRO-seq-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Chlamydomonas_reinhardtii_liquid_culture_5GRO-seq-pooled -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  samtools -paired 
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Chlamydomonas_reinhardtii_liquid_culture_GRO-seq_r1-GSM7439228-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam  SAMstats-Chlamydomonas_reinhardtii_liquid_culture_GRO-seq_r1-GSM7439228 -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  samtools -paired