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-   -   WIG input file for CEAS (Cis-regulatory Element Annotation System) (http://seqanswers.com/forums/showthread.php?t=4550)

clariet 04-01-2010 11:15 AM

WIG input file for CEAS (Cis-regulatory Element Annotation System)
 
I am analyzing a ChIP-seq dataset and want to use CEAS. I have run MACS and got the multiple WIG files (one WIG file for each chromosome and each sample).

But as far as I understand, these WIG files include entire genome, not just peak regions. Anyone has used CEAS before? How could I get a WIG file for peaks identified in MACS?

Thanks a lot!

Clariet

kopi-o 04-02-2010 12:18 AM

MACS will generate a BED file that you should be able to use in CEAS (possibly after slight editing). CEAS does not need a WIG file as input except as an optional choice in the command-line version; the web version only takes a BED file.

You can see an example of the BED file format expected by the web version here:

http://ceas.cbi.pku.edu.cn/example.bed

morganetc 04-07-2010 10:24 AM

command-line
 
Hello,

I actually have the same question, for the command-line CEAS. How to provide the wig file to CEAS, from the multiple wig files returned by MACS ?

Thanks for any hints.

Morgane

bioinfosm 04-09-2010 08:31 AM

Yeah, any chance you could create bed files? Thats simply "chr start stop uniqueID" of your peaks. I just created such a list from my peak finder, and it worked nicely on the CEAS browser.

Only thing, I am not sure what they mean by conservation for the peak region.


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