[mira_talk] Re: SNP detection for genomic sequence
- From: Hanquan Liang <hliang@xxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 6 Jul 2010 13:48:12 -0500
In "The Definitive Guide" (I walked through in a hurry) came with 3.2.0rc1,
SNP detection is mentioned in the sections for "Solexa sequence assembly"
and "EST assembly". In the former case genomic sequence is used, but
reference sequence is also required, While the later case doesn't need any
reference sequence. What the about the case genomic sequence without a
reference? What kind of parameters should I choose?
Sorry If I have missed something in the manual.
H. Liang
On Tue, Jul 6, 2010 at 1:22 PM, Hanquan Liang <hliang@xxxxxxx> wrote:
>
> 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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>
>
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