<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>I'm glad it's working for you. Let us know if you run into additional problems.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Bérénice Benayoun <<a href="mailto:benayoun@stanford.edu">benayoun@stanford.edu</a>><br><span style="font-weight:bold">Date: </span> Thursday, June 27, 2013 8:47 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker and mono-exonic genes ?<br></div><div><br></div>Hi maker devel team,<div><br></div><div>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).</div><div><br></div><div>Thanks for your insights/help !</div><div><br></div><div>Berenice<br><br><div class="gmail_quote">2013/6/10 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>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.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 7 June, 2013 5:32 PM<br><span style="font-weight:bold">To: </span> Bérénice Benayoun <<a href="mailto:benayoun@stanford.edu" target="_blank">benayoun@stanford.edu</a>>, "<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker and mono-exonic genes ?<br></div><div><div class="h5"><div><br></div><div dir="ltr"><div><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.
<div><br>
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><div><br>
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><div><br>
Thanks,</div><div>Daniel<br><div><br><div><font><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></font></div></div><div style="font-size:16px;font-family:Times New Roman"><hr><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></font><br></div><div></div><div>Dear maker developers,
<div><br></div><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><div><br></div><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><div><br></div><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><div><br></div><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><div><br></div><div>Thank you so much in advance for your answer !!!</div><div><br></div><div>Best,</div><div><br></div><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></div></div></div></div></div></div></div></div></div><div class="im">
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<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></span></div></blockquote></div><br><br clear="all"><div><br></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></div></span></body></html>