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reverse complemented reads mapping

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?

sequence alignment
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updated by Ram Ram • written by 332843636 • 332843636

1 answer

Generic aligners always look at both strands unless told otherwise.

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written by Devon Ryan Devon Ryan

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?

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updated by Ram Ram • written by 332843636 • 332843636

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

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written by harold.smith.tarheel harold.smith.tarheel

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