[mira_talk] Re: two different contig with same sequence
- From: "Shai Uliel" <shai@xxxxxxxxxxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 3 Dec 2009 12:26:51 +0200
Hi Bastien
Can you give the explanation when MIRA write SNP (W,R....) and when
MIRA create two contigs ??????
Regards,
Shai.
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Gonzalo Greif
Sent: Tuesday, December 01, 2009 2:09 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: two different contig with same sequence
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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