[mira_talk] Re: SNP detection for genomic sequence
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 7 Jul 2010 00:16:31 +0200
On Dienstag 06 Juli 2010 Hanquan Liang wrote:
> 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?
Time to update the guide I think.
SNP detection *always* works *if* MIRA has info on strains.
Use normal parameters (whichever you use), but telling MIRA to read a
straindata file. In the simplest incantation:
--project=... --job=... -SB:lsd=yes
Indeed, I've made a couple of assemblies with two genomes where one was a
parent and one was a mutagenised child. Works well I think. Though I don't
really know how well it works with more than two strains, but shouldn't be too
bad.
Now, try it out :-)
In the mean time, I've started updating the guide with a section on non-
perfect repeat detection and SNP discovery, but I still need more time
B.
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