When using countOverlaps, it makes counts for each query range, using the subjects. I find the definition of the type = "within" setting non-intuitive. It only counts a subject range if it has a query within it. But since countOverlaps gives one count per query, it seems natural to have gene coordinates as the query object, and short read coordinates as the subject coordinates. Then, using "within" is equivalent to asking how many times each gene is wholly within a short read. Is this a meaningful calculation for other use cases than the one I have made ? Could it be extended to work for the genes and reads scenario ? -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia