[maker-devel] Maker and mono-exonic genes ?

[Carson Holt]

I'm glad it's working for you.  Let us know if you run into additional
problems.

Thanks,
Carson

From:  Bérénice Benayoun <benayoun at stanford.edu>
Date:  Thursday, June 27, 2013 8:47 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Daniel Ence <dence at genetics.utah.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Maker and mono-exonic genes ?

Hi maker devel team,

just wanted to say that retraining SNAP apparently fixed the problem (I
modified the defaults and added "-min-intron 0" to the training everywhere
relevant (default is 30bp, and must prevent single exon genes to be
predicted).

Thanks for your insights/help !

Berenice

2013/6/10 Carson Holt <carsonhh at gmail.com>
> One more note.  The ESTs appear to be from multiple overlapping HSPs (based on
> red line pattern in image).  I'd have to see the actual GFF3 to be sure, but
> if that is the case, then there probably isn't an ORF to work with at that
> location on that strand (so SNAP can't call it).  Possibly the result of
> assembly error or a pseudogene.
> 
> --Carson
> 
> 
> 
> From:  Daniel Ence <dence at genetics.utah.edu>
> Date:  Friday, 7 June, 2013 5:32 PM
> To:  Bérénice Benayoun <benayoun at stanford.edu>, "maker-devel at yandell-lab.org"
> <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Maker and mono-exonic genes ?
> 
> Hi Berenice, Thank you for sending that screenshot and the maker_opts.log
> file. Those are exactly what we need to understand how to expect MAKER to
> perform. 
> 
> In looking at the screenshot, it doesn't look like any of the gene predictors
> gave a prediction in this region. Uses the predictions from ab-initio tools as
> a basis for models and considers models that are supported by evidence. It
> won't by default create a model when there isn't a prediction in the region.
> 
> Can I ask which gene predictors you used and how they were trained? You might
> consider training one or more of them on the specific evidence that you expect
> to support these genes and then rerunning maker with the retrained predictors.
> 
> Thanks,
> Daniel
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Bérénice
> Benayoun [benayoun at stanford.edu]
> Sent: Friday, June 07, 2013 11:17 AM
> To: maker-devel at yandell-lab.org
> Subject: [maker-devel] Maker and mono-exonic genes ?
> 
> Dear maker developers,
> 
> I am currently annotating a de novo fish genome, and have started looking for
> genes of interest in particular in Maker's output to verify that it's
> outputting proper gene sets.
> 
> While many of the genes I look for seem to be correctly annotated by the
> pipeline, I have noticed that important genes that do have strong evidentiary
> support but are monoexonic are NOT reported by maker.
> 
> I am attaching a screenshot for the contig that I know should contain the
> Foxl2 gene (notoriously monoexonic across evolution), and highlighted the
> corresponding evidence for it.
> 
> Is there any setting I can give to maker to force it to output monoexonic
> genes ? I already set "single_exon=1" with no success. I attached my config
> file FYI.
> 
> Thank you so much in advance for your answer !!!
> 
> Best,
> 
> Berenice.
> -- 
> Bérénice A. BENAYOUN, Ph.D.
> Stanford University/Genetics Department
> BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
> M312 Alway Building
> 300, Pasteur Drive
> MC 5120 
> Stanford, CA 94305-5120
> USA
> Email: benayoun at stanford.edu
> Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
> <http://www.stanford.edu/group/brunet/>
> _______________________________________________ maker-devel mailing list
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> er-devel_yandell-lab.org



-- 
Bérénice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>


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