[mira_talk] Re: How does MIRA use paired end information?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 15 Sep 2011 23:46:56 +0200
On Sep 15, 2011, at 23:18 , Evan wrote:
> Bastien, regarding step 2 if MIRA is extending a contig with a read who's
> partner is already contained within the contig being extended are both reads
> equally considered for removal? (IE, perhaps the new read isn't wrong but the
> first read was slightly misplaced)
No, it stays. This can be considered both a strength and a weakness of MIRA.
Strength: there are many libraries which are not, well, ideal in terms of
template sizes. That way one looses only half of the reads. Furthermore, the
read which was placed first was in 99.39845617% of all cases (a number I just
made up now to say "almost always") a read which is not part of a repeat
spanning more than the length of the read. That is: there should be only this
one place in the genome where it could be placed.
Weakness: in the remaining 0.60154382% of the cases (a number I just made up to
say "sometimes shit happens"), the above proves to be wrong. Is likely to occur
only at repeats with two copies in the genome and where sequencing coverage was
(by misfortune) definitively more pointing to non-repetitive instead of
repetitive.
But chances are good that if the first read was misplaced in one of the passes
of MIRA, that read (or a close one nearby) will trigger repeat marker base
detection in case of misalignments, which will help MIRA in the next pass to
avoid that misplacement.
B.
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