WIG input file for CEAS (Cis-regulatory Element Annotation System)

clariet · 04-01-2010, 11:15 AM

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

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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04-01-2010, 11:15 AM	#1
clariet Member Location: NJ Join Date: Mar 2010 Posts: 18	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

04-07-2010, 10:24 AM	#3
morganetc Junior Member Location: berlin Join Date: Apr 2010 Posts: 1	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

04-09-2010, 08:31 AM	#4
bioinfosm Senior Member Location: USA Join Date: Jan 2008 Posts: 482	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. __________________ -- bioinfosm

04-02-2010, 12:18 AM	#2
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	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