[mira_talk] Re: Bivalve EST assembling

  • From: Juan Fernandez Tajes <jfernandezt@xxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 13 Oct 2011 19:57:36 +0200

Hi Bastien,

I´ve tried with Sk:nrr=50 and I´ve increased up to 60 but I get the same 
message: 

"You have 2.61519% of your reads as megahubs. You have set a maximum allowed 
ratio of: 0. Ending the assembly because the maximum ration has been 
reached/surpassed"

Do you think I should try increasing the mmhr? Maybe SK:mmhr=3??

Thanks a lot

Juan
El 13/10/2011, a las 12:53, Bastien Chevreux escribió:

> From: Juan Fernandez Tajes<jfernandezt@xxxxxx>
>> Just in case, I attach the complete repeat ratio histogram....
> 
> Which is way more informative than just the first couple of lines posted 
> previously.
> 
> OK, EST project. Let me guess: you directly went in with nrr=10, right?
> 
> Nothing really extraordinary from the hash statistics, but 10 is definitively 
> too low. Try an assembly with
> 
>  -SK:nrr=50
> 
> and I suppose it would run through. Maybe adjust mmhr, but maybe not 
> necessary.
> 
> B.
> 
> 
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---------------------------------------------------------------
Juan Fernandez Tajes, ph. D
Grupo XENOMAR
Departamento de Biología Celular y Molecular
Facultad de Ciencias-Universidade da Coruña
Tlf. +34 981 167000 ext 2030
e-mail: jfernandezt@xxxxxx
---------------------------------------------------------------




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