bedGraph to bigWig

bdg2bw

#!/bin/bash

# check commands: slopBed, bedGraphToBigWig and bedClip

which bedtools &>/dev/null || { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
which bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
which bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

# end of checking

if [ $# -lt 2 ];then
    echo "Need 2 parameters! <bedgraph> <chrom info>"
    exit
fi

F=$1
G=$2

bedtools slop -i ${F} -g ${G} -b 0 | bedClip stdin ${G} ${F}.clip

LC_COLLATE=C sort -k1,1 -k2,2n ${F}.clip > ${F}.sort.clip

bedGraphToBigWig ${F}.sort.clip ${G} ${F/bdg/bw}

rm -f ${F}.clip ${F}.sort.clip

Hi I have some questions about this script, first, I ran the original script and ran into the error about "Overlapping regions in a BedGraph file", then I made some modifications according to the last post in here and was able to make the bw file. I don't really understand what the codes do....but I was able to make it work.. Do you have further suggestions regarding "Overlapping regions in a BedGraph file"?

In the bw file, I noticed that the "binning" is larger than the original bedgraph, is it possible to keep the original "binning"? It is changed because there's a "bedtool merge" step in the modification (which is to solve the overlapping region error?)?

Thank you!

Hi shannon i don’t really know about the question you described . sorry that i could not be helpful. good day! | | bernie | | ***@***.*** | 签名由网易邮箱大师定制 On 08/26/2022 ***@***.***> wrote： @ShannonTown commented on this gist. Hi I have some questions about this script, first, I ran the original script and ran into the error about "Overlapping regions in a BedGraph file", then I made some modifications according to the last post in here and was able to make the bw file. I don't really understand what the codes do....but I was able to make it work.. Do you have further suggestions regarding "Overlapping regions in a BedGraph file"? In the bw file, I noticed that the "binning" is larger than the original bedgraph, is it possible to keep the original "binning"? Thank you! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>