Difference between Broad and Sharp peaks in chip Seq data

[Ayyappa_kumar]

I would like to understand about the differences between the broad peaks and sharp peaks in chip seq data. What are best tools for finding Broad peaks? Do we need to perform motif detection for the broad peaks (or) we need to study the their effect on the TSS region?

[Dario1984]

Nobody has done an extensive evaluation of competing methods. Choose a recently published method, such as Enriched Domain Detector, which is described in a journal article. It doesn't make sense to do motif finding for broad regions. That's for sharp peaks, such as when the experiment is about transcription factors.