[mira_talk] Re: two different contig with same sequence
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 30 Nov 2009 19:51:51 +0100
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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