Question: reverse complemented reads mapping
0
gravatar for 332843636
3.0 years ago by
3328436360
3328436360 wrote:

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 • 1.2k views
ADD COMMENTlink modified 3.0 years ago by Devon Ryan86k • written 3.0 years ago by 3328436360
1

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.

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum115k
1
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

Generic aligners always look at both strands unless told otherwise.

ADD COMMENTlink written 3.0 years ago by Devon Ryan86k

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? 

ADD REPLYlink written 3.0 years ago by 3328436360
2

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

ADD REPLYlink written 3.0 years ago by harold.smith.tarheel4.2k

I got it. Thank you so much!

ADD REPLYlink written 3.0 years ago by 3328436360
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