reverse complemented reads mapping

Question

[332843636]

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?

[Pierre Lindenbaum]

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.

Answer 1

[Devon Ryan]

Generic aligners always look at both strands unless told otherwise.

[332843636]

Thanks for your answer. I';m a novice in using aligners. I still want to know why they look at both strands of reads. In my mind, the reads in fasta file are all forward, which means they are from 5' to 3'. So is the reference genome. Am I right?

[harold.smith.tarheel]

The references and reads are 5'->3', but DNA is double-stranded. Half of your reads are derived from the complementary (bottom) strand.

[332843636]

I got it. Thank you so much!