zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b1.t1.GGTGAG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d00.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d00.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCGAAT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d00.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d00.RAMPAGE.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d00.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d00.RAMPAGE.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d00.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGGTTA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d05.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d05.GGR.Stanford_Khavari.PAS-seq.b2.t1.TGGCGA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d05.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d05.RAMPAGE.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d05.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d05.RAMPAGE.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d05.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b1.t1.GCGCTG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d10.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d10.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAATGC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d10.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d10.RAMPAGE.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d10.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d10.RAMPAGE.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d10.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b1.t1.GACGAT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d15.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d15.GGR.Stanford_Khavari.PAS-seq.b2.t1.AAGACA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d15.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d15.RAMPAGE.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d15.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d15.RAMPAGE.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d15.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b1.t1.ACCTAC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d20.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d20.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGATG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d20.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b1.t1.AGAATC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d25.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d25.GGR.Stanford_Khavari.PAS-seq.b2.t1.GTTACC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d25.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACCGA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d30.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d30.GGR.Stanford_Khavari.PAS-seq.b2.t1.CAGCGT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d30.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAACAG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d35.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d35.GGR.Stanford_Khavari.PAS-seq.b2.t1.GCAGCC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d35.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b1.t1.CGAAGG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d40.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d40.GGR.Stanford_Khavari.PAS-seq.b2.t1.CGATCT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d40.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b1.t1.AACGCC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d45.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d45.GGR.Stanford_Khavari.PAS-seq.b2.t1.CACTAA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d45.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b1.t1.CAAGCA.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d50.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d50.GGR.Stanford_Khavari.PAS-seq.b2.t1.GGAGGT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d50.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b1.t1.CACACT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d55.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d55.GGR.Stanford_Khavari.PAS-seq.b2.t1.TAATCG.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d55.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b1.t1.TGGATT.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d60.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/primary_keratinocyte-d60.GGR.Stanford_Khavari.PAS-seq.b2.t1.GATCAC.1.fastq.gz | wc -l > raw_read_counts/PAS-seq.primary_keratinocyte-d60.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d20.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d20.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d20.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d20.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d25.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d25.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d25.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d25.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d30.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d30.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d30.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d30.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d35.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d35.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d35.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d35.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d40.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d40.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d40.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d40.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d45.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d45.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d45.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d45.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d50.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d50.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d50.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d50.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d55.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d55.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d55.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d55.b2.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d60.b1.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d60.b1.fastq.lines
zcat /oak/stanford/groups/akundaje/marinovg/Skin_differentiation_project/datasets/reads/RAMPAGE-primary_keratinocyte-d60.b2.end1.fastq.gz | wc -l > raw_read_counts/RAMPAGE-primary_keratinocyte-d60.b2.fastq.lines