[mira_talk] Re: Strange mapping results
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 2 Jul 2010 19:43:17 +0200
On Freitag 02 Juli 2010 Lionel Guy wrote:
> [...]
It's a difficult problem.
Imagine this:
Ref ....caaaag.....
Adding a read with some "junk" you my get:
Ref ....c**aaaag.....
R1 ....ccaaaaag.....
Now comes a couple of reads with the terminal "a"
Ref ....c**aaaag.....
R1 ....ccaaaaag.....
R2a ....ca
R2b ....ca
R2c ....ca
Which is the most optimal solution from a mathematical point of view for a
Smith-Waterman alignment, because
Ref ....c**aaaag.....
R1 ....ccaaaaag.....
R2a ....c*a
R2b ....c*a
R2c ....c*a
or even
Ref ....c**aaaag.....
R1 ....ccaaaaag.....
R2a ....c**a
R2b ....c**a
R2c ....c**a
are mathematically less optimal for each individual read, although it does
make more sense in the complete alignment that way.
To be honest, I don't have a really good solution for that (and I tried quite
a lot). Fortunately, 36mers are a thing of the past, 75 and 100mers take over
and there the problem is much less pronounced.
B.
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