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Genomic Distribution Of Peaks

Hi!

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

Thank you

chip-seq data analysis
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updated by Biostar Biostar • written by Dataminer Dataminer

2 answers

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/

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written by Chris Whelan Chris Whelan

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

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written by Dataminer Dataminer

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).

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written by Benm Benm

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.

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written by Dataminer Dataminer

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