Hi Austin,
As you mention, the difference could be related to how much of the query
sequence is actually aligned and passes summary filters. It all depends
on the query data, reference genome, and the parameters used for
alignment and summary tools.
If you do think that a problem exists with
Just to emphasize the point, the difference between the two methods is an
order of magnitude (for a particular example, filtering for flag type gives
around 60% of reads mapping, but estimating mapped reads from pileup gave
~5% of reads mapped).
Thanks,
Austin
On Tue, Sep 6, 2011 at 8:40 AM, Aust
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