python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py fft2fft3-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/2019-02-06-PomBase.fixed.gtf 200 200 100 fft2fft3-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters-V2.py wt-pooled-STAR-2.5.3a/STAR-2.5.3a-Aligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/Schizosaccharomyces_pombe.ASM294v2.20.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/Fungi/Schizosaccharomyces_pombe.ASM294v2/2019-02-06-PomBase.fixed.gtf 200 200 100 wt-pooled-STAR-2.5.3a.RAMPAGE-clusters-V2.bed