Hi,
I would like to ask if any of you have experience with generating *WIG
coverage files from PE ssRNA-Seq* data. I got some discussion around this (
http://seqanswers.com/forums/showthread.php?t=20545) but it seems not to be
solved yet.
Also, does *countOverlaps* function work with GappedAlignmentPairs object?
In that case, will the first or last alignment of each pair be used for
calculating the overlap?
Thanks much in advance.
Best,

	[[alternative HTML version deleted]]

