python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d00.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d00.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d05.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d05.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d10.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d10.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d15.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d15.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d20.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d20.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d25.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d25.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d30.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d30.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d35.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d35.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d40.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d40.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d45.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d45.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d50.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d50.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d55.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d55.RAMPAGE.b2.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d60.RAMPAGE.b1.snglt1.dedup
python /oak/stanford/groups/akundaje/marinovg/code/transcriptome/RAMPAGE-clusters.py primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.sortedByCoord.out.dedup.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/hg19.chrom.sizes /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/gencode.v19.annotation.gtf 200 50 1 RAMPAGE-primary_keratinocyte-d60.RAMPAGE.b2.snglt1.dedup