[mira_talk] Re: hyrbid assembly with yeast 454 paired end reads and sanger reads in exp format

On Wednesday 25 February 2009 -alreza- wrote:
> I have a question on running hybrid assemblies. I am running a hybrid
> assembly with yeast 454 Paired end reads (Titanium machine) and Sanger
>  reads which are in EXP format. Now these sanger EXP files are separate
> files for each read. Would MIRA be able to run the hybrid assembly if the
> EXP reads are kept separated (there are 17664 of these EXP files)?

Absolutely. You just need to tell MIRA that the Sanger data must be loaded 
from EXP files, the list of which being in a file of file names. E.g.:

  mira --project=myproject --job=denovo,genome,normal,sanger,454 
            -LR:sanft=fofnexp

(+ any other parameters you might want or need, like e.g. -DI:exp and -
DIR:scf)

Regards,
  Bastien


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