Question: Chipseq overlap of peaks
1
gravatar for kanwarjag
5.0 years ago by
kanwarjag1.1k
United States
kanwarjag1.1k wrote:

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 grp of databases. I have seen lot of tools which may allow quarrying expression data bases, however I dont 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 • 2.0k views
ADD COMMENTlink written 5.0 years ago by kanwarjag1.1k

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

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.0 years ago by Fidel2.0k
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