[maker-devel] failed gene prediction

[Jason Stajich]

For fungi, I've put up some of the gene prediction parameters that I've built or trained if that is a helpful for you.

https://github.com/hyphaltip/fungi-gene-prediction-params

In the absence of any ESTs or RNA-Seq I also recommend generating a starting training set with CEGMA first and then training your predictors from there except for GeneMark.hmm which seems to do okay with self-training.

Jason
On Mar 18, 2013, at 10:49 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You didn't supply any evidence or HMM files for gene predictors.  Just raw assembly data by itself is insufficient for genome annotation.
> 
> Here is some nice documentation for running MAKER  --> http://gmod.org/wiki/MAKER_Tutorial_2012
> Here is a nice overview of genome annotation ion general --> http://fasta.bioch.virginia.edu/cshl/pdf/12/ajm12/euk_genome_annotation_review.pdf
> 
> Once you've gone through the documentation and examples, if you come across any questions just let us know.
> 
> Thanks,
> Carson
> 
> 
> From: "Borhan, Hossein" <Hossein.Borhan at AGR.GC.CA>
> Date: Monday, 18 March, 2013 4:40 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] failed gene prediction
> 
> Hi
> 
> I have tried maker on a fungus genome of 45 mb with 1/3 being repeat rich. It did not produce any prediction. I am not sure what is causing this. Attached are  the STDERR and opts.ctl.  I appreciate your help
> 
> 
> Hossein
> 
> 
> 
> 
> 
> 
> 
> 
> 
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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