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?
Hello 332843636!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=186933
This is typically not recommended as it runs the risk of annoying people in both communities.