Question: Whole Genome Wig To Bigwig
0
gravatar for Radhouane Aniba
7.5 years ago by
Radhouane Aniba750 wrote:

Hello everyone,

I am using QuEST for my Chip-Seq data analysis, and one of its features is that it produces a whole genome wig.gz file, and also by chromosome.

The entire genome wig is too large to be uploaded as custom track to UCSC genome browser, is ther any method to convert it into bigwig ? (the whole genome one, I took a look at wigtobigwig utility but it looks like it works only on chromosomes)

Cheers

Rad

wiggle bigwig • 3.8k views
ADD COMMENTlink modified 7.5 years ago by Hanfei Sun60 • written 7.5 years ago by Radhouane Aniba750
3

you can get chrom.sizes like (change hg19 to your organism): mysql --user=genome --host=genome-mysql.cse.ucsc.edu -ANe "select chrom, size from hg19.chromInfo" > chrom.sizes

ADD REPLYlink written 7.5 years ago by brentp23k
2

wigToBigWig works fine with wig files of the entire genome, so it will do what you want.

ADD REPLYlink written 7.5 years ago by Brad Chapman9.4k

I don't understand "it looks like it works only on chromosomes".

ADD REPLYlink written 7.5 years ago by Pierre Lindenbaum119k

Thank you Brad I will try it, in their readme they say wigToBigWig in.wig chrom.sizes out.bw, in case of entire genome what will be the chrom.sizes ?

Pierre I meant individual chromosomes

ADD REPLYlink written 7.5 years ago by Radhouane Aniba750

working great. Thank you very much

ADD REPLYlink written 7.5 years ago by Radhouane Aniba750
0
gravatar for Hanfei Sun
6.9 years ago by
Hanfei Sun60
Boston
Hanfei Sun60 wrote:

Use bx-python developed by James taylor

https://bitbucket.org/james_taylor/bx-python/wiki/Home

ADD COMMENTlink written 6.9 years ago by Hanfei Sun60
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