Chipseq overlap of peaks
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6.9 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 • 2.5k views
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I think that EpiExplorer may be able to do what you want, but only for a selected and preprocessed number of features.

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