[maker-devel] Augustus retraining??

[Mikael Brandström Durling]

Hi,


14 jan 2015 kl. 09:49 skrev Xabier Vázquez Campos <xvazquezc at gmail.com<mailto:xvazquezc at gmail.com>>:

Hi,

I trained Augustus using the output of CEGMA (http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.CEGMATraining) through WebAugustus, which makes the training very easy but, and here is my question, can/should I re-train Augustus like it is done with SNAP? And what would I use for the re-training

I’ve tried an approach of retraining augustus in a manner similar to what has been suggested here earlier for retraining of SNAP. This has been run with a local augustus installation as part of an automated framework I have set up to annotate fungal genomes. Interestingly, augustus seems to converge very quickly. It is not uncommon that autoAugustus reports that it could not improve the initial models that were derived from the CEGMA dataset. Are there other similar experiences on the list?

I also a modified version of maker2zff which I call maker2augustus_gff which extracts an evidence set for augustus retraining from the initial round of maker. I’m happy to share it with anyone interested.

cheers,
Mikael



Thank you,

Xabier
--
Xabier Vázquez Campos
PhD Candidate
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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