Chips-seq replicates and motif discovery: how to deal with the merged peaks?

[feralBiologist]

I have chip-seq triplicate (3 treatment, 3 controls, each of the 6 with their input control). I have identified the peaks using macs14 for each sample and its input control. Than I performed differential binding analysis using diffBind. It produced a set of (merged) peaks (peak consensus). Now I would like to proceed with the motif discovery using meme-chip or rsat.

What is methodically most sound way to go for motif discovery from the merged peaks/peak consensus?

AFAIK meme-chip/rsat expect relatively narrow summit sequences whereas diffBind merges peaks and so produces longer peak sequences. Shall I de-merge the consensus peaks? Or merge all treatment samples into a single sample and define the peaks from it? My uncertainty stems from the fact that motif discovery tools seem to expect a single sample, rather than a set of replicates each introducing some noise and variation in the peak location (and some lacking some of the peaks altogether).

[rory]

This depends on whether you are looking to do de novo motif discovery or are looking for enrichment of known motifs. We find that the latter is generally more useful for the types of questions we are asking. We use the dreme module of meme-chip for this and it works fine for the wider peaks derived from DiffBind. meme (plus tom-tom to match known motifs) will also work for discovery, but the resultant motifs are less precise than they could be.

In the next version of DiffBind, we are looking at implementing a feature that will allow you to "center" the peaks around the summit and return them all with a defined size (e.g. 250bp on each side) -- that should help for this type of analysis.

-Rory