[maker-devel] Augustus retraining

[Panos Ioannidis]

Hi Xabier,

Thanks for your quick reply!

No, I haven't used WebAugustus, but I just checked it out and it looks like
my training set is too big (~300 Mbp), so I can't even upload it!

Anyway, I prefer to train it locally because I have better control over
each step. Also, I have done the entire training procedure with less genes,
but didn't get a good gene-level sensitivity (~5%). So now I'm trying to
replicate it using more of my scaffolds, but as it appears I get a lot more
incomplete models from exonerate (run through Maker).

P



On Tue, Mar 24, 2015 at 1:06 PM, Xabier Vázquez Campos <xvazquezc at gmail.com>
wrote:

> 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/20150324/2be728f0/attachment-0003.html>