[mira_talk] Re: Alignment errors in Solexa mapping
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Dec 2009 19:49:48 +0100
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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