determine if ChIP-seq peaks are broad or narrow Is there a method to determine if the peaks are broad or narrow? ENCODE provides some guidelines:



Although those cover common histone marks, there are many others. If you are using one of the ones that are not listed, is there a way to determine the appropriate peak width?

This question was inspired by this previous post.
I'd say mostly this is a question of understanding the underlying biology and the relevant literature. 

If it is not known in the literature whether a mark is peaky or broad, evidence might come from FISH studies or Low throughput qPCR. Another way to look would be to examine the signal expressed as fold enrichment over input on a genome browser and look if peaks tended to be small (a few hundred bp, e.g. a transcription factor), or large (several 1kb, e.g. H3K27me3) or contain both (e.g. RNA polymerase II).