python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d0.RNA-seq_polyA.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d0.RNA-seq_polyA.b2
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d3.RNA-seq_polyA.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d3.RNA-seq_polyA.b2
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d6.RNA-seq_polyA.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d6.RNA-seq_polyA.b2
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d0.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d0.RNA-seq_ribozero.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d0.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d0.RNA-seq_ribozero.b2
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.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 - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d3.RNA-seq_ribozero.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d3.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d3.RNA-seq_ribozero.b2
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d6.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d6.RNA-seq_ribozero.b1
python /oak/stanford/groups/akundaje/marinovg/code/BAMtoFASTQ.py primary_keratinocyte-d6.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes - -ignoreChromSizes | python /oak/stanford/groups/akundaje/marinovg/code/assembly/SortPEFASTQ.py - primary_keratinocyte-d6.RNA-seq_ribozero.b2