[mira_talk] Re: SNP detection for genomic sequence
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 6 Jul 2010 19:27:23 +0200
Hi,
2010/7/6 Kalyan K Pasumarthy <kalyankpy@xxxxxxxxx>
> Hi,
>
> 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.
>
IMHO that is not perfectly true. When I denovo-assemble my ESTs from e.g.
different tissues or individuals I can of course look for SNPs. SNPs are
simply (true) differences in pools of sequences between difefrent tissues,
idividuals, strain or species (or whatever).
Or between a set of sequences and a reference sequence ...
cheers,
Sven
> On 6 July 2010 22:15, Hanquan Liang <hliang@xxxxxxx> wrote:
>
>> Greetings,
>>
>> Can I use mira to search SNPs/mutations in genomic sequence data, without
>> reference sequence? Genomic sequencing results usually generate longer
>> contigs, or maybe lower coverage sometimes. I'm concerning if mira can
>> handle the problem(s) in such case. Anyone has experience or advice?
>>
>> Thanks
>>
>> H. Liang
>>
>
>
>
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