/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d00.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d00.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d00.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d00.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d05.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d05.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d05.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d05.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d10.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d10.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d10.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d10.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d15.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d15.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d15.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d15.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d20.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d20.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d20.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d20.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d25.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d25.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d25.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d25.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d30.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d30.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d30.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d30.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d35.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d35.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d35.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d35.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d40.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d40.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d40.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d40.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d45.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d45.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d45.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d45.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d50.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d50.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d50.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d50.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d55.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d55.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d55.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d55.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d60.RAMPAGE.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d60.RAMPAGE.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments --paired-end -p 8 primary_keratinocyte-d60.RAMPAGE.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d60.RAMPAGE.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d00.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d00.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d00.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d00.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d05.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d05.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d05.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d05.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d10.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d10.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d10.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d10.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d15.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d15.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d15.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d15.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d20.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d20.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d20.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d20.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d25.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d25.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d25.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d25.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d30.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d30.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d30.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d30.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d35.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d35.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d35.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d35.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d40.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d40.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d40.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d40.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d45.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d45.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d45.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d45.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d50.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d50.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d50.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d50.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d55.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d55.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d55.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d55.PAS-seq.b2/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d60.PAS-seq.b1/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d60.PAS-seq.b1/RSEM-from-STAR
/oak/stanford/groups/akundaje/marinovg/programs/RSEM-1.3.0/rsem-calculate-expression --alignments -p 8 primary_keratinocyte-d60.PAS-seq.b2/STAR-2.5.3aAligned.toTranscriptome.out.bam /oak/stanford/groups/akundaje/marinovg/genomes/hg19/gencode/gencode_v19/RSEM/gencode_v19  primary_keratinocyte-d60.PAS-seq.b2/RSEM-from-STAR