[mira_talk] Re: Alignment errors in Solexa mapping
- From: Björn Nystedt <bjorn.nystedt@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Dec 2009 08:36:18 +0100
> 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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