[maker-devel] what is a 'model file' for the web annotation service?

[Carson Holt]

Also it’s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.

—Carson



> On Jun 24, 2016, at 7:22 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. 
> 
> On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu <mailto:sullis02 at nyu.edu>> wrote:
> Sorry if this is a dumb question.
> 
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input
> 
> I generated a  training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):
> 
> 
> 
> Species parameter archive:  parameters.tar.gz
> 
> Training genes:  training.gb.gz
> 
> Ab initio predictions:  ab_initio.tar.gz
> 
> predictions with hints:  hints_pred.tar.gz
> 
> 
> 
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.
> 
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.
> 
> Do you know which file would be correct for input to online MAKER as a 'model' file?
> 
> 
> (NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )
> 
> 
> 
> 
> 
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