13 months ago by
CRUK, Cambridge, UK
For histone marks that have broad enrichment there is no magic number for this analysis. Are you using "broad" peaks (eg from MACS)?
Something to keep in mind is that the peak width doesn't need to encompass the entire enriched area to do a differential binding analysis. Using the
summits parameter in this situation should result in a maximally enriched representative region being used for the comparison. So long as the same interval is used for all samples (which
DiffBind will do automatically), the analysis should be reasonable, so it doesn't matter that much so long as the value is comfortably within the actual "peak" widths.
My practical advice here is to try the analysis both ways (with and without the
summits parameter). To set the
summits parameter, you may want to look at your distribution of peak widths and choose a value accordingly, e.g. the minimum or first quartile value.
For example in the sample dataset:
Min. 1st Qu. Median Mean 3rd Qu. Max.
310.0 706.0 830.0 961.4 1073.0 5251.0
you can see that
summits=250 results in intervals of 500bp, which is somewhere between the minimum and the first quartile.