BAM coverage, paired-end data, overlapping mates: is there double-counting?
I have a question about the following scenario. If I generate a coverage
wiggle_xyplot track from a bam file that comes from a paired-end
dataset, what happens if a read pair has overlapping mates? Will the
overlapping region from this pair contribute a count of 1 to the
coverage (which would be the correct way of doing this) or will there be