[mira_talk] Re: Denovo versus mappings assembly with Mira
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Sun, 12 May 2013 10:56:12 -0400
I am wondeing, after denovo on a diploid organism, would a mapping allow for
the differentiation between the two haploid states?
Sincerely,
Adrian
On 2013-05-12, at 12:13 AM, David Coil <coil.david@xxxxxxxxx> wrote:
> Thank you so much for the detailed and rapid response Bastien... it's
> extremely helpful!
>
>
> If you take the current default FASTA output from a mapping assembly in MIRA
> you get something many people do not expect: an amalgam of the data from your
> mapped strain and, in coverage holes, the data from the reference. I thought
> this to be a good idea, but I'm not so sure anymore.
>
> I did fail to catch that the FASTA output of the large contig contained
> sequence from the backbone. It makes total sense for what one might use
> mapping for, but did create the false illusion for me of having a kick-ass
> assembly. :)
>
> What one should do with the results from mapping: use convert_project to
> extract the clean "by strain" data. Like this:
>
> convert_project -f maf -t fasta mira_out.maf mynewresults
>
> Thank you, I'll do that.
>
>
> -David
>
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