[maker-devel] Augustus training for new species

[Xabier Vázquez Campos]

Is it a plant genome? If it isn't, use BUSCO. It will do the whole training
in a single step. It will get your assembly fasta file and generate the
species profile in the Augustus species folder.

See previous thread:
https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ


If you have a plant genome, use the "zff2augustus_gbk.pl".
I have this in my files:

This will take the export.dna generated by fathom and generate a *.gb file
> that will be used as "training gene structure file" in a new training
> submission in WebAugustus, but remember to give it a new name in the
> submission, e.g. MYGENOME_v2, or Maker won't see the difference (same
> name)*:
>
    perl PATH/TO/SCRIPT/zff2augustus_gbk.pl > MYGENOME.train.gb
>

*this applies if you do a re-run of Augustus within Maker

On 28 April 2016 at 11:04, hcma <hcma at uci.edu> wrote:

> Hi,
>
> I would like to use Maker to generate a set for training Augustus for a
> new species. The steps for training SNAP is well documented, but i am still
> confused as to how to train Augustus using the AugustusWeb.
>
> I have used fathom and forge to generate 'export.ann' and 'export.dna'. So
> what i need to do next is to run zff2augustus_gbk.pl in the directory
> that has the export.ann and export.dna files?
>
> Then i feed the train.gb file to  AugustusWeb?
>
> Please advise.
>
> Thanks
> Karen
>
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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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