[mira_talk] Re: two different contig with same sequence
- From: Gonzalo Greif <gonzalo.greif@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 1 Dec 2009 10:08:42 -0200
I will see in more details the two contig, but probably the answer resolve
my question,
so, thank you very much
Gonzalo
2009/11/30 Bastien Chevreux <bach@xxxxxxxxxxxx>
> On Montag 30 November 2009 Gonzalo Greif wrote:
> > I take two different consensus contigs from mira, and i perform the
> > alignement with sanger sequence using blast, and the match is 99% or
> > something like this.
>
> Then MIRA decided that these were different ESTs.
>
> Imagine this simple case: a gene has two slightly different alleles and
> you've
> sequenced this:
>
> A1-1 ...........T...........
> A1-2 ...........T...........
> A1-3 ...........T...........
> A1-4 ...........T...........
> A1-5 ...........T...........
> A2-1 ...........G...........
> A2-2 ...........G...........
> A2-3 ...........G...........
> A2-4 ...........G...........
>
> MIRA will recognise that there's enough evidence for a T and also enough
> evidence for a G at that position and create two contigs, one containing
> the
> "T" allel, one the "G". The consensus will be >99% identical, but not 100%.
>
> From there on, you can build more complicated cases but I'll leave it to
> anyones imagination what kind of other cases can arise (especially funny
> when
> starting to take sequencing errors into account *sigh*).
>
> Does this answer your question?
>
> Regards,
> Bastien
>
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