Hi Rong- You are correct that the peak merging logic results in wider peak areas that may incorporate multiple binding sites and/or make it more difficult to determine the precise binding site. This is true of the peak calling step as well. In our experience, the scientific questions we are actually asking do not require the precise binding location in the differential analysis step -- we are first looking for places where there is a significant difference in binding levels. It is only after that, and only in a minority of cases, that we look to narrow the region down to a specific binding site of interest (eg, to find enriched motifs). Tehre are a numebr of tools available to find more narrow, precise binding sites in a set of candidate regions. The most recent release of DiffBind does, however, include some features to better a) focus on the likely binding site and b) work with more uniform, narrower peak widths. It accomplishes this using the "summits" parameter in dba.count. This parameter allows you to identify the "summit" for each peak interval (the point of highest pileup), and optionally re-center the peaks around this point (eg, taking 200bp upstream and downstream of the summit for each merged peak; summits=200). If there were several "true" binding sites in a merged peak, you are likely to end up with only one of them, but the results are more consistent overall. Cheers- Rory On 12/05/2014 17:40, "Rong Cong" <rong.cong at="" inserm.fr=""> wrote: >Hi Rory, >Thank you very much for your patient and efficient reply to my naive >question. The short version answer made me quite clear of the idea. > >Indeed, overlapping and merging peaks may form a quite wider peak to be >compared among different peaksets, but for biologists, the wider peak >often has no meaning to us(some biologically functional elements are >quite short),therefore is it possible for DiffBind to adjust some >parameters to narrow a little the overlapped and merged peak for >comparison? (Again, I am not a bioinformatician, sorry for this naive >question.) >Looking forward to your reply. >All the best, >Rong >