Use in ChIP Seq Analysis

[jesswhitts]

Hello,

I was just wondering what you would recommend when trying to integrate peak calling pipelines with RepEnrich. We want to generate a set of ChIP peaks which we can identify as overlapping with TE regions or not.

Should we call peaks on the full bam file (uniquely mapped and multimapped reads), or just the uniquely mapped ones?

Many thanks,
Jess