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

[Bérénice Benayoun]

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/>
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