Hi

How does one work with coverage on GappedAlignmentPairs  in the context of
RNASeq?
The simplest way is to consider each left and right read as separate -
essentially loose the "paired" information and calculate coverage.
However, if both the left and right pair reads fall within a feature of
interest - say an exon, does it imply coverage of the region of the exon
between the reads too

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
  LLLLLLLLLL---------------------------RRRRRRRRRR
                    ^^^^^^^^^^^^^^^^^

In the figure above, the exon is represented by ">" and L and R represents
the left and right reads aligned to the exon.
I am talking about the region represented by "^".  Do we assume coverage
for this region too?
Does Coverage on GappedAlignmentPairs do this?

-best
-Lax
Center for Neuroscience Research
Tufts Univeristy School of Medicine
Boston, MA

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