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, Austin Paul <austi...@usc.edu> wrote:

> Hello,
>
> I recently figured out how to filter the output bwa SAM file for flag type
> in order to determine the number of reads that were successfully mapped.  My
> question is, I previously thought I could generate a pileup, then sum the
> number of counts for each base of the reference, and divide this number by
> the length of the reads (not exact if some reads are hanging over the edge
> of the reference sequence, but should be close?).  But when I compare these
> methods, I get drastically different results.  What am I missing?
>
> Thanks,
> Austin
>
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