[maker-devel] Augustus retraining

[Xabier Vázquez Campos]

Hi Panos,

Have you tried using webAugustus for the (re)training? I found it very
convenient for generating the models for Augustus.

Cheers,

2015-03-24 19:29 GMT+11:00 Panos Ioannidis <panos.ioannidis at gmail.com>:

> Hello All,
>
> I'm trying to retrain Augustus using EST data from the same species and
> realized that quite a few of the gene models I get based on EST data are
> incomplete (i.e. no start and/or stop codon).
>
> Now, when I get to the "etraining" step in Augustus retraining (right
> after the time-consuming "optimize_augustus.pl" step), I get a warning
> for each gene that doesn't contain a start or stop codon.
>
> .....
> gene maker-scaffold4|size2210279-exonerate_est2genome-gene-20.1-mRNA-1
> transcr. 1 in sequence scaffold4|size2210279_2021791-2044735: Initial exon
> does not begin with start codon but with acg
> gene maker-scaffold4|size2210279-exonerate_est2genome-gene-20.2-mRNA-1
> transcr. 1 in sequence scaffold4|size2210279_2045713-2064983: Terminal exon
> doesn't end in stop codon. Variable stopCodonExcludedFromCDS set right?
> ....
>
> Does anyone know whether training is compromised by such incomplete gene
> models? Do you usually exclude them from the training set?
>
> Oh, and by the way, the best guide to retraining Augustus is here
> <http://avrilomics.blogspot.ch/2013/04/training-augustus-gene-finding-software.html>.
> The official
> <http://bioinf.uni-greifswald.de/augustus/binaries/retraining.html> web
> page isn't bad, but doesn't explain in detail certain things.
>
> Thanks,
> Panos
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
Xabier Vázquez Campos
*PhD Candidate*
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150324/0b0a4daf/attachment-0003.html>