How to get enrichment of ERVs in differentially expressed peaks from ATAC-seq data?

Question

[fdemiguelsdp]

Hi folks,

I performed ATAC-seq after knock-down of a chromatin remodeling factor and I have plenty of peaks that are differentially expressed (more or less accessible regions). Some other data indicates that there may be an antiviral response going on in the cells so I'd like to see if somehow the ERVs are being exposed in the chromatin upon knock-down.

How would you suggest I perform this task? Thank you!

[pb11]

Have you figured this out? I am looking to do similar analysis.