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Extract a chromosome from a WIG file

I have a large WIG files which are difficult to run in IGV, due to the size. I am only interested in chromosome M so I would like to extract signal from that chromosome and thus have a smaller file size. I found one solution on Stackoverflow (https://stackoverflow.com/questions/17354962/pcregrep-a-wiggle-file-to-extract-chromosome-multiple-line-regex-search), but that doesn't work at all. Any other ideas? I check UCSC utils and extensively searched online. I am also open to suggestions on bedgraph or similar formats.

wig
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updated by haizi.zh • haizi.zh • written by Fluorine Fluorine

but that doesn't work at all

Please specify what doesn't work.

The awksolution on stackoverflow looks fine to me.

fin swimmer

• 1 views • link
written by finswimmer finswimmer

It produces an empty file. I checked with grep and the chromosome exists in the original file.

• 1 views • link
written by Fluorine Fluorine

3 answers

use one of the tools provided by the UCSC to extract a region of the chromosome : http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

for example bigWigToWig :

   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

and then convert back to bigwig with wigToBigWig

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. I knew there had to be a simple solution like this available.

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written by Fluorine Fluorine

Here's another solution.

You can convert the wig file to a bedGraph using bedops and manually cutting it:

wig2bed < hg19.sometrack.chr21.wig | cut -f1-3,5 > hg19.sometrack.chr21.bedgraph

Then convert it back to bigWig:

bedGraphToBigWig hg19.sometrack.chr21.bedgraph hg19.sizes hg19.sometrack.chr21.bw
• 0 views • link
written by haizi.zh • haizi.zh

Try IGV 'toTDF' to convert your 'WIG' files into binary tiled data (TDF). This loads into IGV lot faster than 'WIG' files.

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written by EagleEye EagleEye

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