How to compare two WIG files??

[tfcheng]

Hi all,
Sorry if this is an faq question... I been doing chip-seq for a while, I perform chip and other people in the lab do seq, actually. So I don't really know what's going on in the black box. After GA-II, I have 23 WIG files that can be uploaded to UCSC genome browser for me to examine. And that was just preliminary exp, now I have control vs. experimental chip-seq, and I need to extract the difference between them, I am not exactly a bioinformatics guy, so I come up here and ask for help in terms of the software that I can use, thank you!!

TFC

[pmad]

HI TFC,

the Bioconductor package NarrowPeaks

http://bioconductor.org/packages/release/bioc/html/NarrowPeaks.html

can handles comparison of bigWig files, but you will need to covert WIG to bigWig using the wigToBigWig utility (http://genome.ucsc.edu/goldenPath/help/bigWig.html)

Hope that helps,
P.