I've done this with Velvet scaffolds, that contain long runs of N's between
contigs. Are the newbler scaffolds straight fasta? Or are there dashes or
other odd characters in there? Lower case (not sure if that'd cause a
problem for MAUVE)?
~Joe
On Wed, Jan 26, 2011 at 5:41 AM, Nick Loman <n.j.lo...@bham.ac.uk> wrote:
> Hi mauve-users
>
> Mauve doesn't seem to much like aligning scaffolds from 454 assemblies
> (where contigs are joined by long runs of Ns). It complains that the
> sequence has gaps or is already aligned.
>
> Can it be made to play ball? I'd much rather use scaffolding information
> where available than reordering contigs.
>
> Cheers
>
> Nick
>
>
>
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--
Joseph Fass
Bioinformatics Programmer
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
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