Creates stranded BigWig files from BED

make_bw_from_bed.sh

#!/bin/bash
chromsizes="./chrom.sizes"
genomeCoverageBed=`which genomeCoverageBed`
bedGraphToBigWig=`which bedGraphToBigWig`
vis="./vis"
samples=9
fromsample=1
rep=2
fromrep=1

if ! [ -f "$chromsizes" ]; then
        echo "chrom.sizes file not found"
        exit 2
fi

mkdir -p $vis

for s in $(seq $fromsample $samples)
do
        for r in $(seq $fromrep $rep)
        do
                sample=D${s}_R${r}
                echo processing $sample

                $genomeCoverageBed -bg -i ${sample}.pos.bed -g ${chromsizes} -strand + > ${vis}/${sample}.pos.bg 
                $genomeCoverageBed -bg -i ${sample}.neg.bed -g ${chromsizes} -strand - > ${vis}/${sample}.neg.bg.1 
                cat ${vis}/${sample}.neg.bg.1 | awk '{ $4 = - $4 ; print $0 }' > ${vis}/${sample}.neg.bg && rm ${vis}/${sample}.neg.bg.1
                $bedGraphToBigWig ${vis}/${sample}.pos.bg ${chromsizes}  ${vis}/${sample}.pos.bw &
                $bedGraphToBigWig ${vis}/${sample}.neg.bg ${chromsizes}  ${vis}/${sample}.neg.bw &
        done
done