Convert BedGraph to bigWig

bdg2bw.sh

#!/bin/bash
#$ -N dg2bw
#$ -cwd
#$ -q long-sl7,mem_512_12h,mem_512
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G
#$ -o bdg2bw.out
#$ -pe smp 8
#$ -j y

bdg2bw () {
  local bdg=$1
  local bdgsort=${bdg%%bdg}sorted.bdg
  local bw=${bdg%%bdg}bw
  echo $(date): Sorting and converting $bdg
  bedSort $bdg $bdgsort
  bedGraphToBigWig $bdgsort $chrom $bw
}
chrom=/no_backup/asebe/genome_db/Nvec/Nvec_gDNA_concat_mito.fasta.sizes
bdgs=$( ls /users/asebe/aelek/proj/ATACseq_nvec_*/*/alignments/*bwa.shift.nucfree.bdg )
for bdg in $bdgs; do bdg2bw "$bdg"; done