sample_prep.sh

#! /bin/bash

chroms=("chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22")
#chips=("shsy5y.par.atmi.ppois" "shsy5y.par.dmso.ppois" "shsy5y.rchip.atmi.ppois" "shsy5y.rchip.dmso.ppois" "shsy5y.atac.SRR5819663_SRR5819664_treat_pileup" "shsy5y.ctcf.SRR6334830.ppois" "shsy5y.h3k27ac.SRR3363257.ppois" "shsy5y.h3k27me3.SRR3363258.ppois" "shsy5y.h3k4me1.SRR3363256.ppois" "shsy5y.h3k4me3.SRR3363255.ppois" "shsy5y.igg.SRR4291521_SRR4291522.ppois" "shsy5y.pol2.SRR6322542_SRR6322543.ppois" "shsy5y.s96.SRR4291525_SRR4291526.ppois")
chips=("shsy5y.rchip.atmi_nac.ppois" "shsy5y.rchip.dmso_nac.ppois" )

for chip in ${chips[@]}; do
  for chrom in ${chroms[@]}; do
    awk -F'\t' -v awkvar="$chrom" '{if ($1==awkvar) print $0}' ./inputs/SHSY5Y/$chip.bdg > ./inputs/SHSY5Y/prepped/$chip.$chrom.bdg
  done
done