Question: Intersection of bigwig and bed files
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gravatar for palabari
8 days ago by
palabari10
palabari10 wrote:

I have uploaded bigwig data from GEO to UCSC. I have a set of genomic regions of interest as bed and I would like to find out whether these regions intersect with ATAC-Seq peaks in the bigwig data.

If I simply use the Table Browser intersection tool, I get regions with peaks that are very small, and probably not significant.

I assume that I have to filter by the peak's size. Here is where I have most questions because I am unsure of how to perform this step. I know that the bigwig files have been normalized and scores represent 1 × 10^7 reads. However, I do not know what peak size would be correct to assume it is a real "peak". Is there a tool to do this? Is there any standard protocol to follow? Am I thinking this correctly or is there any other way to solve this?

Thank you.

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