[mira_talk] Re: scaffolded contigs
- From: Adnan Niazi <niazi84@xxxxxxxxxxx>
- To: mira talk <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 21 Jul 2010 17:52:15 +0000
> 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.
Yes, i will try it, but i am afraid as I read that convert project will list
the desired coverage contigs in multifasta format and it will not insert N's
between the contigs. For example: Zero coverage region b/w two contigs is 200bp
long, so there should be 200 N's b/w contigs in fasta file.
But i will have to check it before saying anything.
Regards
/adnan
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