Hi, I have a question about the peak calling step. Broad peaks are called by default, I was wondering what is the recommendation for peak calling settings if there are different marks (some have narrow and some broad)? Does one need to run the pipeline separately per mark?

Hi Nima, No, you can run different sized peaks within the same run. In principle, based on personal experience, macs3 in broad peak mode should also call narrower chip seq target peaks. However, peak summits are not reported in broad peak mode and you might get merged proximal narrow peaks, if that is sufficient for you go a head. Since peak calling might be anyway iterative, I would give it a first run with the defaults and adapt the peak calling accordingly.

Hi Kevin! Thanks for your response. It was very informative.