[maker-devel] Training Augustus

[Jason Stajich]

Muriel -

Be best if you take longest models - ones that have ATG and STOP — my workflow is to analyze the data with Trinity to assemble the transcripts (genome guided) and then align these transcripts to the genome with PASA and take the longest ORFs using scripts provided with PASA to generate the best set for gene predictions.


> On Oct 28, 2014, at 3:04 AM, Muriel Gros-Balthazard <muriel.grosb at gmail.com> wrote:
> 
> Hello !
> 
> I want to train Augustus for a non model organism and I have several questions about it !
> 
> I planned to follow the section "Training ab initio Gene predictors".
> 
> So first, I need to generate a gene model using EST data.
> However, I was wondering how many sequences are necessary ?
> Indeed, my genome is 476 Mb and I have milllions of RNA seq data but it takes ages if I put all of them !
> I tried with 1000 sequences and it takes 30 min but is that enought ? Or should I take more ?
> 
> Secondly, we then obtain plenty of gff files, should we concatenate them ?
> 
> And then, what to do ? Indeed, the help of maker explains for Snap, but I want to use Augustus.
> I found a script called autoAug.pl to train Augustus.
> What do you think of it ?
> 
> Should I use it that way ?
> autoAug.pl --singleCPU --useexisting --genome=mygenome.fasta --species=myspeciesname --cdna=EST.fasta --trainingset=genome.gff3
> 
> 
> where EST.fasta is the file I used earlier to generate the gene model and genome.gff3 is the result of the gene model.
> However, I don't think that I obtained gff3 file from the first maker run.
> So should I generate gff3 from gff ???
> 
> Thanks a lot for your help,
> 
> Muriel
> 
> 
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