Whole Genome Wig To Bigwig

Question

[Radhouane Aniba]

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

[brentp]

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

[Brad Chapman]

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

[Pierre Lindenbaum]

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

[Radhouane Aniba]

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

[Radhouane Aniba]

working great. Thank you very much

Answer 1

[Hanfei Sun]

Use bx-python developed by James taylor

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