[maker-devel] BUSCO

[Dolze, Florian]

On a somewhat related note, is there an advantage of using BUSCO to 
train Augustus instead of the provided Augustus webtraining service? 
Does anybody know how those 2 compare?


Am 13.05.2016 um 09:56 schrieb Panos Ioannidis:
> Hello Ian,
>
> Xabier is right. You have to run BUSCO with the --long switch and 
> then, in the maker_opts.ctl file, you should point the 
> augustus_species variable to your trained species (i.e. the name you 
> pass with the -o/-a parameter).
>
> So, in Xabier's example your maker_opts.ctl file should contain the 
> following line:
>
> augustus_species=Genus_species
>
> Felipe, Rob, is there something else that I'm missing? Truth is that I 
> haven't run this recently and there might be differences in newer 
> BUSCO versions.
>
> Panos
>
>
> Panos Ioannidis, PhD
> Postdoctoral researcher
> Computational Evolutionary Genomics Group
> University of Geneva
>
> On Fri, May 13, 2016 at 2:31 AM, Xabier Vázquez Campos 
> <xvazquezc at gmail.com <mailto:xvazquezc at gmail.com>> wrote:
>
>     Check this thread:
>     https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ
>     <https://groups.google.com/forum/#%21topic/maker-devel/vp8R06VVQGQ>
>
>     On 26 April 2016 at 02:20, Misner, Ian (NIH/NIAID) [C]
>     <ian.misner at nih.gov <mailto:ian.misner at nih.gov>> wrote:
>
>         Hello,
>
>         Are there any guidelines for using BUSCO to help train MAKER?
>         CEGMA has been discontinued but I used to use the cegma2zff.pl
>         <http://cegma2zff.pl> steps to use those proteins as a
>         training step. BUSCO seems to train Augustus but I'm not sure
>         what file to pass from BUSCO to MAKER for this to be properly
>         utilized. I didn't see anything specific about this in the
>         archives.
>         -----
>
>         *Ian Misner, Ph.D.*
>
>         Computational Genomics Specialist
>
>         Contractor, Medical Science and Computing, Inc.
>
>         Bioinformatics and Computational Biosciences Branch (BCBB)
>
>         NIH/NIAID/OD/OSMO/OCICB
>
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>
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>
>     -- 
>     Xabier Vázquez-Campos, /PhD/
>     /Research Associate/
>     Water Research Centre
>     School of Civil and Environmental Engineering
>     The University of New South Wales
>     Sydney NSW 2052 AUSTRALIA
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