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I use some mainstream aligners (BWA, Razers3) to map human's single-end reads to hg19. And I notice that some reverse complemented reads map to the reference in the result SAM file, for FLAG is set to be 16 or 272 (256+16) in some of the alignment result. I am confused about when do the aligners reverse complement input reads and map them. Do the aligners always do this job or they just do this when a read in forward fails to map on the reference?
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cross posted: https://www.biostars.org/p/170836/ -
Devon Ryan on Biostars told me that Generic aligners always look at both strands unless told otherwise. Then harold.smith.tarheel explained that this is because DNA is double-stranded. That's exactly what I was confused about.Last edited by howen; 12-29-2015, 05:18 PM.Comment
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