python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py 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 /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5_genomic.gtf  200 100 500  Chlamydomonas_reinhardtii_liquid_culture_5GRO-seq-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py 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 /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5_genomic.gtf  200 100 500  Chlamydomonas_reinhardtii_liquid_culture_GRO-seq_r1-GSM7439228-STAR-2.5.3a.RAMPAGE-clusters-V2.bed