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<div class="PlainText">Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div id="divRpF42143" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> berenice.benayoun@gmail.com [berenice.benayoun@gmail.com] on behalf of Bérénice Benayoun [benayoun@stanford.edu]<br>
<b>Sent:</b> Friday, June 07, 2013 3:50 PM<br>
<b>To:</b> Daniel Ence<br>
<b>Subject:</b> Re: [maker-devel] Maker and mono-exonic genes ?<br>
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<div>Hi Daniel,
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<div>Thanks for the quick answer !</div>
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<div>I used SNAP, and trained from a hmm model made with the CEGMA output on my genome (240 gene models) plus a first run of maker of 1/3 of the genome. I tried GenemarkES and Augustus, but for some reason they don't run, so I stopped indicating their existence
to maker.</div>
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<div>Should I do something in particular to train it "better" ? Is there any other predictor that would be worth running ? </div>
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<div>Thanks so much for your help !</div>
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<div>Berenice<br>
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<div class="gmail_quote">2013/6/7 Daniel Ence <span dir="ltr"><<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>></span><br>
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<div style="direction:ltr; font-size:10pt; font-family:Tahoma">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.
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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. </div>
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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. </div>
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Thanks,</div>
<div>Daniel<br>
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<div>Daniel Ence<br>
Graduate Student<br>
Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330</div>
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> maker-devel [<a href="mailto:maker-devel-bounces@yandell-lab.org" target="_blank">maker-devel-bounces@yandell-lab.org</a>] on behalf of Bérénice Benayoun [<a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a>]<br>
<b>Sent:</b> Friday, June 07, 2013 11:17 AM<br>
<b>To:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a><br>
<b>Subject:</b> [maker-devel] Maker and mono-exonic genes ?<br>
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<div>Dear maker developers,
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<div>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.</div>
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<div>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. </div>
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<div>I am attaching a screenshot for the contig that I know should contain the <i>
Foxl2</i> gene (notoriously monoexonic across evolution), and highlighted the corresponding evidence for it.</div>
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<div>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.</div>
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<div>Thank you so much in advance for your answer !!!</div>
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<div>Best,</div>
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<div>Berenice.</div>
<div>-- <br>
<font>Bérénice A. BENAYOUN, Ph.D.</font><br>
Stanford University/Genetics Department<br>
<i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>
M312 Alway Building<br>
300, Pasteur Drive<br>
<span>MC 5120 <br>
Stanford, CA 94305-5120</span><br>
USA<br>
Email: <a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>
Web: <a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a>
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-- <br>
<font>Bérénice A. BENAYOUN, Ph.D.</font><br>
Stanford University/Genetics Department<br>
<i>BRUNET Laboratory</i>, 'Molecular Basis of Longevity and Age Related Diseases'<br>
M312 Alway Building<br>
300, Pasteur Drive<br>
<span>MC 5120 <br>
Stanford, CA 94305-5120</span><br>
USA<br>
Email: <a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a><br>
Web: <a href="http://www.stanford.edu/group/brunet/" target="_blank">www.stanford.edu/group/brunet/</a><a href="http://www.stanford.edu/group/brunet/" target="_blank"></a>
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