python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py S_cerevisiae_WT_PROcap-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/sacCer3.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/Saccharomyces_cerevisiae.SacCer_Apr2011.20.TIF-seq-updated-V3.gtf 200 200 100 S_cerevisiae_WT_PROcap-STAR-2.5.3a.RAMPAGE-clusters-V2.bed