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

[Bérénice Benayoun]

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/>
> _______________________________________________ maker-devel mailing list
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>



-- 
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/>
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