Hi All

Just wanted to check on the expected behavior of the summarizeOverlaps
function in the GenomicRanges package for the following cases.


1. In the case of paired end data does it count each read pair as 1 or 2
against a feature.

2. For stranded protocols of RNA-Seq does it take it account the opposite
strand of the mate of a read when counting or does it take only one read
matching the strand into consideration.

3. For second strand RNA-Seq protocol where the read-1 matches to the
opposite strand of gene will summarizeOverlap work ?

Thanks!
-Abhi

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