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Question: How to annotate peaks inside TADs and annotated with Gene expression?
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I have a dataset of Chip-seq and RNA-seq experiments, there's also available HI-C data from the same stage and condition, I would like to annotate the nearest gene that is within TAD boundaries, Which method would you suggest to do this kind of analysis? I'm doing it just by annotating both coordinates form chip and RNA seq in same "clusters" and then annotated by nearby gene intra-tad. If there's a current workflow you know or some library please comment.

Thank you!

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