[maker-devel] Augustus retraining

[Panos Ioannidis]

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
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