Hello

My question is similar to this one Minimum overlap for summarizeOverlaps() to call hit

suppose I have read of length (100bp) and I use summarizeOverlap() mode= Union what is the minimum overlap between read and target feature to count hit i.e how may basepairs should hit the feature to count as hit...

That's a pretty thorough discussion on the page you reference. In one of the responses I specify that overlap only requires one base.

Are you also using bedtools? Are you seeing some kind of inconsistency? It would be good to see a code example if you have a specific question.

Valerie
 

Edit: Specifically, look at Martin's GRanges example on Minimum overlap for summarizeOverlaps() to call hit . Try creating your own GRanges, perform the overlaps and see if the answer makes sense.