Hi
My apologies for multiple posting if it happens-- I sent the last mails
from other accounts which may not be registered with Bioc-list
-Lax
Two questions:

1. Is readGapppedAlignmentPairs - the most efficient way to read a
paired-end bam file with mulit-mapped reads?
I am asking as it takes an enormous amount of time to process and load.

2. 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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