python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py RAMPAGE_IRBB7_Control-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.gtf 200 200 100 RAMPAGE_IRBB7_Control-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py RAMPAGE_IRBB7_Treated-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Oryza_sativa/Oryza_sativa.MSU6.19.fixed.gtf 200 200 100 RAMPAGE_IRBB7_Treated-STAR-2.5.3a.RAMPAGE-clusters-V2.bed