[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 

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.


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