When using summarizeOverlaps to count reads overlapping a particular feature, what is the minimum number of bases required to overlap in order to be called a hit (ie. 1 base, 2 bases, 3 bases)? I'm using mode="Union", inter.feature="FALSE" (ie. type="any"), ignore.strand=FALSE.
I'm curious because I am also using bedtools (v 2.25) coverage command to determine the %sequence coverage of the particular feature, and the read counts I get from bedtools is different from summarizeOverlaps for many loci (some are actually the same). By default bedtools coverage uses 1 base overlap necessary for a hit to be called. I've also made sure that bedtools coverage is assessing the exact same loci as summarizeOverlaps.