[maker-devel] BUSCO

[Robert Waterhouse]

I think in the Augustus 'species' directory there should be a new folder
named according to your BUSCO run, and in that folder should be the trained
parameters for your new species, so from MAKER I guess you can point to
these trained parameters.

Rob


  \\      Dr Robert Waterhouse
O0o--    SIB maître assistant
  ""    www.rmwaterhouse.org

A maturing understanding of the composition of the insect gene repertoire COIS
2015 <http://www.sciencedirect.com/science/article/pii/S2214574515000073>
BUSCO: assessing genome assembly and annotation completeness Bioinformatics
2015
<http://bioinformatics.oxfordjournals.org/content/early/2015/06/27/bioinformatics.btv351.full>

On 13 May 2016 at 09:56, Panos Ioannidis <panos.ioannidis at gmail.com> wrote:

> 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> wrote:
>
>> Check this thread:
>> https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ
>>
>> On 26 April 2016 at 02:20, Misner, Ian (NIH/NIAID) [C] <
>> 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 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)
>>>
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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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