8 weeks ago by
University of Cambridge, Cancer Research UK - Cambridge Institute
Yes, I would use the summits option in DiffBind to analyze these data.
This is straightforward for the H3K4me3 mark, which is generally narrow. For the other marks, which tend to be enriched over a wider intervals, generally the important thing is to accurately detect changes in enrichment in the vicinity of a certain genomics features (enhancer, TSS, etc). The summits parameter works by finding a point of optimal enrichment among all the samples where enrichment was identified, then creating a consistent window around that point which is used to detect differential enrichment. It is usually more important that the window being tested represents a representative region truly enriched in at least one sample group, than to represent the entire enriched region. Even if it is a subset of the full enriched region, if it is changing significantly between sample groups, that tells you what you need to know about enrichment in/near that feature. If you try to cover the entire region of enrichment, you will include more "background" bases that are not truly enriched, and this noise dilutes the confidence statistics.
Ultimately it depends on exactly what your experiment is designed for; there are some cases where knowing the precise boundaries of enrichment are more important, in which case you may lose some information by re-centering the consensus peaks.