Chipseq overlap of peaks
0
1
Entering edit mode
8.9 years ago
kanwarjag ★ 1.2k

I have chipseq coordinates (of course peak score) which are differential enriched in my experiment. I want to overlap these regions with some publicly available Chipseq data. I do understand the usual process will be take raw data align call peak with same algorithm which I have used and then intersect with tools like bedtools.

However, as you see it is a quite time consuming process, What I am looking for is quick online tool/ database to at least roughly tell me which whether my peaks will show some percentage of overlap with specified GEO number or a group of databases. I have seen lot of tools which may allow quarrying expression data bases, however I don't know any which may be useful for Chipseq peaks. My online search lead to

https://genome.ucsc.edu/encode/FAQ/#release4

I want to check if experts may have better tools or option or someone may have used above link successfully.

Thanks for any pointers.

ChIP-Seq • 2.9k views
ADD COMMENT
0
Entering edit mode

I think that EpiExplorer may be able to do what you want, but only for a selected and preprocessed number of features.

ADD REPLY

Login before adding your answer.

Traffic: 831 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6