[mira_talk] Re: Extracting contigs from mapped assembly / convert_project output
- From: Surya Saha <ss2489@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 27 May 2013 17:53:45 -0400
Thanks much, Bastien
On Monday, May 27, 2013, Bastien Chevreux wrote:
> On May 27, 2013, at 20:31 , Surya Saha <ss2489@xxxxxxxxxxx <javascript:;>>
> wrote:
> > I get the following unpadded files -
> > XXX_default.unpadded.fasta
> > XXX_StrainX.unpadded.fasta
> > XXX_ReferenceStrain.unpadded.fasta
> > XXX_AllStrains.unpadded.fasta
> >
> > I can figure out that ReferenceStrain is the backbone. What is the
> difference between the three other files? They have very similar
> characteristics. Thanks
>
> - "default" you please forget.
> - "StrainX" is the strain of your mapped reads (which you could have
> renamed to whatever you had wanted via MIRA command line / parameter file)
> - "ReferenceStrain" is indeed your reference / backbone
> - "AllStrain" is a merge between all strains (in this case: reference and
> strainx) where bases with "N" in the strainx data are filled with bases
> from the reference strain (if present)
>
> B.
>
>
>
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--
-----------------------------------------------------
Surya Saha
Department of Plant Pathology
and Plant-Microbe Biology
Cornell University, NY, USA
http://www.linkedin.com/in/suryasaha
Twitter: @SahaSurya
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