RepEnTools and other recommendations?

[JustJosu3]

I'm working on a project that involves analyzing ChIP-seq data, and I'm particularly interested in looking at protein enrichment on repetitive DNA sequences. My research led me to discover RepEnTools and it seems promising, especially with the automated workflows and focus on REs. I'm curious if anyone here has used it yet and what your experience has been?

I'm trying to decide on the best approach for this analysis and would love to hear any recommendations or advice you might have. Are there other tools out there that you've found to be particularly effective for handling multi-mapping reads and accurately quantifying signal on repeats? Any feedback on RepEnTools, or suggestions for alternative pipelines or software, would be a huge help! Thanks in advance!

 

[TropicalMe]

I've tested RepEnTools but just briefly so not enough to form a strong opinion, but from the little I encountered, it handled RE-focused analysis really well, especially with multi mappers.

 

[Darwin's intern]

Chasing protein enrichment on repetitive DNA is kind of a waste of time, most of that signal is noise. RepEnTools might look slick, but any accurate quantification there is probably overhyped.