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

[Daniel Ence]

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<mailto:benayoun at stanford.edu>
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