[mira_talk] RE Re: scaffolded contigs
- From: Jorge.DUARTE@xxxxxxxxxxxx
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 21 Jul 2010 16:48:39 +0200
> Why program yourself if it's already present?
>
> Adnan: if you used strain information for your reads, try
>
> convert_project -f (maf or caf) -t fasta ...
>
> which will output different FASTAs for each strain present in the
> assembly. Then grep the FASTAs for the '@' sign ... these are the
> places where no read from a given strain covers the place.
Hi Bastien,
since you talk about using convert_project to get fasta format from caf,
i'd like to ask you if it would be possible to get also the mixed strains
consensus sequences as an output instead or in supplement of the strain
specific consensi ?
Many times i used convert_project to extract only the contigs with a
minimum coverage (using option -y),
but it is not possible to generate something similar to the unpadded fasta
file generated by mira
in de _d_results directory. Is there a reason for that ?
Thanks for your reply
jorge.
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