this is very useful but why when blast one of the unordered contigs it shows
100% similarity to the reference (but it was not aligned properly by Mauve.
Also, can see a contig at the middle of the graph that has no similarity to the
reference strain (not at the right side_- is this possible?
> From: aaron.darl...@uts.edu.au
> To: mauve-users@lists.sourceforge.net
> Date: Mon, 26 May 2014 19:38:14 +1000
> Subject: Re: [Mauve-users] MCM unordered contigs
>
> Hi Mariam,
> Perhaps the easiest way to do this is via the graphical interface. If
> you load the final alignment generated by the contig mover in the Mauve
> viewer, any unplaced contigs will appear on the right side of the draft
> genome track. They will be unaligned, and therefore will not have any
> similarity plot or connecting lines to the reference genome. If you
> hover the mouse over one of those contigs its name will appear in the
> lower right corner of the window.
> If you need an automated approach you might be able to base it off of
> the _contigs.tab file in the output directory, which describes what was
> done with each contig at each reorder iteration.
>
> Best,
> -Aaron
>
> On Fri, 2014-05-23 at 09:30 -0500, Mariam Iskander wrote:
> > Hello,
> >
> > I am using MCM to order some contigs, and I would like to exclude the
> > contigs with no ordering information associated with them. According
> > to the User Guide, the contigs with no LCBs are included at the end of
> > the genome, but I could not figure out where the ordered contigs end
> > and the unordered ones begin. I looked through the output files and I
> > couldn't find this information. Is it possible to get the list of
> > contigs with no LCBs?
> >
> > Thank you very much.
> >
> > Mariam
> >
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> Aaron E. Darling, Ph.D.
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> University of Technology Sydney
> Australia
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