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 a SAMTools utility itself, or have a detailed question about the exact algorithm used, you may want to send an email to the tool authors and see what they think.
http://samtools.sourceforge.net/

Thanks!

Jen
Galaxy team

On 9/6/11 1:02 PM, Austin Paul wrote:
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
<mailto: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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