[mira_talk] Re: Homopolymer errors and MIRA
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 26 Sep 2009 17:20:09 +0200
On Freitag 18 September 2009 Lionel Guy wrote:
> [...]
Hi Lionel,
hrm, let me guess: Newbler 2.x? Last time I made a (admittedly very rough)
comparison was with the 1.x line of Newbler and there things looked a bit
better for MIRA. Well, Newbler improved :-)
Anyway, the numbers you show are pretty interesting. As MIRA strictly follows
a "majority wins" strategy for calling (or not) bases at homopolymer sites,
the numbers show that the 454 basecaller has a tendency to undercall
homopolymers. I suspected that, but it's anyway good to know.
What I'd be interested in would be this: do you have some statistics which
show the errors broken down by homopolymer length. I strongly suspect that
longer homopolymers are more prone to the base calling error, so shifting
calling weights according to homopolymer length is probably one possible
solution. Ideally there would also be statistics which show how many
gaps/bases were at each erroneous site, but that might be a bit too much to
ask.
Happy holidays,
Bastien
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