Re: [Bio-bwa-help] Reverse-forward oriented reads

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

In some way, maq is a good choice for Illumina's jumping library as it
properly deals with both FR short-insert pairs and RF long-insert
pairs. Many other aligners only handle one type of pairs, which is not
optimal at least in theory.

Heng

On Wed, Apr 28, 2010 at 03:00:00PM -0400, Adrian Heilbut wrote:
> BWA does NOT currently handle them -  Heng Li has confirmed it - eg see:
> http://seqanswers.com/forums/showthread.php?t=4523&highlight=jumping
> 
> I've had much better luck using MAQ for this, which seems to work for all
> possible orientations, and checks both strands automatically.  If you need
> the speed, Bowtie also lets you explicitly specify the expected
> orientations.  For both, it is necessary to also specify the max insert
> sizes that you expect to get sensible results.
> 
> Adrian
> 
> On Wed, Apr 28, 2010 at 2:39 PM, Shaun Jackman <sja...@bc...> wrote:
> 
> > Hi,
> >
> > I'd like to align reads that have reverse-forward (RF) orientation from
> > the Illumina circular fragment protocol. Can BWA detect that the reads
> > are RF and "do the right thing". Alternatively, is there an option to
> > specify that the reads should be oriented RF?
> >
> > If none of the above, will reverse complementing the reads prior to
> > alignment have the desired effect?
> >
> > Thanks,
> > Shaun
> >
> >
> >
> >
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