[mira_talk] Re: eukaryotic cDNA: assembler parameterization pipeline

  • From: Jose Blanca <jblanca@xxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 4 Jun 2009 12:19:46 +0200

On Thursday 04 June 2009 11:52:05 Jan Paces wrote:
> hi alexie,
>
> Alexie Papanicolaou wrote:
> > I've written a short pipeline for parameterization of MIRA for cDNA data.
> >
> > Essentially, it launches MIRA and Newbler with an array of parameters
> > (from a simple config file) and saves the user from defining many times.
> > Once they finish the script conducts a BLASTX approach to identity
> > contig quality. It's all pretty automated so i when i come to work in
> > the morning my run has finished :-)
>
> it looks useful. can you, please, point me where to download it?
>
> thanks,
>
> jan

Hi:
I'm also interested in looking at how your have done it. 
By the way I'm also storing (or trying to) ESTs and unigenes in to a Chado db. 
I'm writting a script to go from the caf file to the chado db in one go.
Best regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)

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