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).