python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d30.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d30.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.plus.wig -fragments first-read-strand -stranded + -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d30.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d30.b2.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.wig -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d35.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d35.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.plus.wig -fragments first-read-strand -stranded + -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d35.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d35.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.wig -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d3.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d3.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.wig -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d40.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d40.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.plus.wig -fragments first-read-strand -stranded + -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d40.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d40.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.wig -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py ==== primary_keratinocyte-d55.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d55.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.end1.5p.minus.wig -end1only -stranded - -notitle -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.wig -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.plus.wig -fragments first-read-strand -stranded + -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/makewigglefromBAM-NH.py ==== primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.minus.wig -fragments first-read-strand -stranded - -RPM -notitle
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py ==== primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.end1.5p.plus.wig -end1only -stranded + -notitle -RPM &
python /oak/stanford/groups/akundaje/marinovg/code/make5primeWigglefromBAM-NH.py ==== primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes primary_keratinocyte-d25.b1.RAMPAGE/STAR-2.5.3aAligned.sortedByCoord.out.end1.5p.minus.wig -end1only -stranded - -notitle -RPM &