Genomic Distribution Of Peaks

Question

[Dataminer]

Hi!

Is their any web application to determine genomic distribution of peaks (for the peak file generated by MACS)?

Thank you

Answer 1

[Chris Whelan]

I've used CEAS to do this, also from the Liu lab (the same folks responsible for MACS):

http://liulab.dfci.harvard.edu/CEAS/

Personally I've downloaded the program to run locally, but I think there's an online version available in a Galaxy installation at:

http://cistrome.org/ap/

[Dataminer]

I am also using the web based version of CEAS through Galaxy/Cistrome and I was wondering if any other similar tool was available.

Answer 2

[Benm]

Do you mean you want to see these peak? Maybe UCSC Genome Browser can help you, refers to Shirley Pepke, Barbara Wold & Ali Mortazavi, Computation for ChIP-seq and RNA-seq studies. Nature Methods 6, S22 - S32 (2009).

[Dataminer]

No, I want to know number of peaks present in each genomic region. As an example consider you have 9000 peaks called by MACS, I want to know out of these 9000 thousand peaks how many are present in promoter region, intron, and intergenic regions.