python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d00.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d00.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d00.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d00.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d05.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d05.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d05.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d05.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d0.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d0.RNA-seq_polyA.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d0.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d0.RNA-seq_polyA.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d0.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d0.RNA-seq_ribozero.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d0.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d0.RNA-seq_ribozero.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d10.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d10.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d10.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d10.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d15.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d15.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d15.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d15.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d20.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d20.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d20.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d20.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d25.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d25.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d25.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d25.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d30.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d30.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d30.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d30.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d35.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d35.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d35.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d35.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d3.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d3.RNA-seq_polyA.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d3.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d3.RNA-seq_polyA.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d3.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d3.RNA-seq_ribozero.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d3.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d3.RNA-seq_ribozero.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d40.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d40.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d40.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d40.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d45.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d45.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d45.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d45.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d50.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d50.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d50.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d50.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d55.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d55.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d55.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d55.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d60.PAS-seq.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d60.PAS-seq.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d60.RAMPAGE.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d60.RAMPAGE.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d6.RNA-seq_polyA.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d6.RNA-seq_polyA.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d6.RNA-seq_polyA.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d6.RNA-seq_polyA.b2 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d6.RNA-seq_ribozero.b1/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d6.RNA-seq_ribozero.b1 -RPM
python /oak/stanford/groups/akundaje/marinovg/code/bedRPKMfromBAM.py gencode.v19.annotation.TSS500bp-Exon-Intron-Intergenic-partition 0 primary_keratinocyte-d6.RNA-seq_ribozero.b2/STAR-2.5.3aAligned.sortedByCoord.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes gencode.v19.annotation.partition.RPM.primary_keratinocyte-d6.RNA-seq_ribozero.b2 -RPM