Re: [Bio-bwa-help] no reverse mapping needed

[Heng Li <lh...@sa...>]

On Apr 25, 2012, at 2:12 PM, nn1 wrote:

> Hi all,
> 
> I am not interested in reverse or complementary matches. If the query
> is, say, "ACCGT", I am interested only in references that have "ACCGT",
> not
> the one that have "TGGCA". Is the "-c" parameter the one I need?

Option -c (only available in bwa-0.5.x) sort of does the thing you want, but not exactly. It aligns the read and the reversed but not complemented read. Supposedly, few reversed reads can be aligned.

Heng

> 
> cheers,
> Nick
> 
> 
> 
> 
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-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.