[mira_talk] Re: SNP detection for genomic sequence
- From: Hanquan Liang <hliang@xxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 6 Jul 2010 13:22:46 -0500
On Tue, Jul 6, 2010 at 12:52 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> On Dienstag 06 Juli 2010 Peter wrote:
> > > An SNP or a mutation it self is defined as a change from the reference
> > > sequence. So, I believe it is not possible to define an SNP with out a
> > > reference sequence.
> >
> > You could still look for a SNP relative to the contig consensus. e.g. If
> > most of the reads give an A but some give a C, that could be a SNP.
>
> At least with MIRA, you'd need to compare closely matching contigs with
> each
> other as MIRA will have dutifully built a contig with the "A" and another
> with
> the "C". When not knowing which strain the reads come from, MIRA will treat
> that as repeat marker and separate.
>
This is the feature of MIRA.
>
> On the other hand, if MIRA knows that the reads with the A are all
> "strain1"
> and those with "C" are all "strain2", it will mark this as a SNP.
I used miraSearchESTSNPs for ESTs assembly before. It showed me SNPs in the
output. But Now I have another project for detecting SNPs from several
different (but related) GENOMEs, not ESTs.
Since miraSearchESTSNPs is programed for EST which is shorter than genomic
contigs, I think Bastien have a reason(s) for including "EST" in the program
name. And I have the question: besides the EST cases, can I
use miraSearchESTSNPs for detecting SNPs in genomic data?. I would like the
way MIRA marks SNPs for me :)
>
> B.
>
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