[mira_talk] Re: mapping assembly -> memory problem

  • From: Alexie Papanicolaou <alpapan@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 05 Jan 2010 12:22:52 +0000

Not to mention it will be extremely slow ;-)

Google for smth like EST genome alignment and there are quite a few
solutions. EMBOSS's standard est2genome is quite good but I would first
create contigs of the ESTs and then map them. It has also been built for
rather inbred data... estwise from Birney is a good tool. One thing you
can do is use nucmer to detect any misassemblies.


a

On Tue, 2009-12-22 at 16:05 +0100, Bastien Chevreux wrote:

> On another note: mapping ESTs to a genome will not work well as MIRA doesn't 
> do splicing, I need to document that in the docs. You might want to use other 
> mappers for this task.
> 
> Regards,
>   Bastien
> 

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