Question: Extracting Reads Mapped From Bwa Mapping
0
Austin Paul • 140 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