[mira_talk] Re: Alignment errors in Solexa mapping

> As long as what you show me are two reads and not the reference and a read, 
> I'm fine. I don't like it, but I've learned that whatever clever trick one 
> applies, there will always be a combination of mapping sequence and 
> sequencing 
> errors that will lead to situations like this.

You are right, the situtation occurs at homopolymer frameshifts in the 
reference, so exactly as you describe below. Sorry for being slow :)

> I have an idea how this kind of effect could be toned down a bit and the 
> pieces for it are almost in place in MIRA, but I need to test it (and hope it 
> really works).

That sounds great!

B




On Fri, 11 Dec 2009 19:49:48 +0100
Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Freitag 11 Dezember 2009 Björn Nystedt wrote:
> > I am still somewhat confused about exactly how the second error can occur.
> >  The situation is that this is what you would expect 
> >  ...CATTTTTTC...
> >      ATTTTTTC...
> > but this is what you get
> >   ...CATTTTTTC...
> >      A*TTTTTTC...
> > I can see the point of relaxing gap penalties at ends of reads, but to
> >  prefer a mismatch over a match seems strange to me. Note also that there
> >  was no IUPAC in the reference in this case!
> 
> As long as what you show me are two reads and not the reference and a read, 
> I'm fine. I don't like it, but I've learned that whatever clever trick one 
> applies, there will always be a combination of mapping sequence and 
> sequencing 
> errors that will lead to situations like this.
> Welcome to the wonderful world of mapping.
> 
> Imagine you have a backbone:
> 
> B   ...GCTTTTTTCG...
> 
> You now map the first read which has one sequencing error right at the 
> beginning/end (an A instead of a C):
> 
> B     ...GCTTTTTTCG...
> r1        ATTTTTTCG...
> 
> Now you map a second read, where the sequecning error is an insertion (an 
> additional A) somewhere in the middle of the read. Remember, you map against 
> the reference:
> 
> B     ...GC*TTTTTTCG...
> r1        A*TTTTTTCG...
> r2    ...GCATTTTTTCG...
> 
> Wham! You have the situation you described. From there on, things can only 
> deteriorate with additional reads :-)
> 
> I have an idea how this kind of effect could be toned down a bit and the 
> pieces for it are almost in place in MIRA, but I need to test it (and hope it 
> really works).
> 
> Regards,
>   Bastien
> 
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-- 
====================================
Björn Nystedt, PhD
Molecular Evolution
EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala
Sweden
phone: +46 (0)18-471 45 88
email: Bjorn.Nystedt@xxxxxxxxx
====================================

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