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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Thanks, I had a mistake in the command line!!!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><br>
Claudio<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Daniel Ence [mailto:dence@genetics.utah.edu]
<br>
<b>Sent:</b> woensdag 19 februari 2014 17:04<br>
<b>To:</b> Valero Jimenez, Claudio; 'Carson Holt'; Carson Holt; 'maker-devel@yandell-lab.org'<br>
<b>Subject:</b> RE: [maker-devel] Maker not predicting many genes<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi Claudio,
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">What was the command line you used for gff3_merge?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Daniel<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">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<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> maker-devel [maker-devel-bounces@yandell-lab.org]
on behalf of Valero Jimenez, Claudio [claudio.valero@wur.nl]<br>
<b>Sent:</b> Wednesday, February 19, 2014 1:20 AM<br>
<b>To:</b> 'Carson Holt'; Carson Holt; 'maker-devel@yandell-lab.org'<br>
<b>Subject:</b> Re: [maker-devel] Maker not predicting many genes</span><span style="font-size:12.0pt;font-family:"Times New Roman","serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Hi Carson,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Thank you for your suggestions. I ran again Maker and it was able to predict many more genes. Although I have a different problem now. I try to run gff3_merge
and get the following error: </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Use of uninitialized value $outfile in substitution (s///) at ./gff3_merge line 67.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Similar thing happens when I try fasta_merge:</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Use of uninitialized value $outfile in substitution (s///) at ./fasta_merge line 52.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">I never had this problem before with these commands.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Regards,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Claudio</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Carson Holt [<a href="mailto:carsonhh@gmail.com">mailto:carsonhh@gmail.com</a>]
<br>
<b>Sent:</b> maandag 17 februari 2014 20:26<br>
<b>To:</b> Carson Holt; Valero Jimenez, Claudio; 'maker-devel@yandell-lab.org'<br>
<b>Subject:</b> Re: [maker-devel] Maker not predicting many genes</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">From your control file, it looks like not setting single_exon=1, and only using UniProt rather than supplying complete proteomes of a related species are your primary shortcomings. I’d set correct_est_fusion=1
as well.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">—Carson</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Carson Holt <<a href="mailto:carson.holt@genetics.utah.edu" target="_blank">carson.holt@genetics.utah.edu</a>><br>
<b>Date: </b>Monday, February 17, 2014 at 12:22 PM<br>
<b>To: </b>"Valero Jimenez, Claudio" <<a href="mailto:claudio.valero@wur.nl" target="_blank">claudio.valero@wur.nl</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>
<b>Subject: </b>Re: [maker-devel] Maker not predicting many genes<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">You also need to look at the contigs in a browser like apollo. That will allow you to see both the predictions and the evidence in context. You can then see if genes are being dropped because
they are only being supported by single exon evidence, they have no evidence support whatsoever, or if they are being excluded because of UTR overlap. That last one is a common problem for fungi when using assembled mRNA-seq reads. Fungi genes are so close
that they often overlap in the UTR. As a result, mRNA-seq assemblers falsely asseble neighboring genes into single transcripts. The result is really long UTR on some of your gene models that force other models to be excluded. If this is the case, rerun
something like trinity with the jacquard clip option set to avoid transcript fusion. Then set correct_est_fusion=1 in the MAKER control files to get those long false UTR’s clipped off.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">If it is a lack of evidence overlap, make sure you provided minimum 1 proteome from a related species to the protein= option. At least 2 proteomes are recommended though (these are not proteins
from the same species but rather complete proteomes from related species). Also comprehensive databases like UniProt/Swiss-prot are not sufficient on their own, but can supplement the other proteome data. Also are you providing EST data? Note that EST/mRNA-seq
data without a proteome from a related species is also not siufficient (because both quality and how comprehensive EST/mRNA-seq databsases are can vary so widely, and may only capture as little as 30% of the genes).</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Another thing that comes into play are single exon evidence. In anything but fungi, single exon evidence is mostly caused by spurious alignments. But fungi have so many single exon genes, that
this is not the case for them. Make sure single_exon=1 is set to allow that evidence to be kept, and set the length of single exon evidence to keep to something like 250 bp.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Thanks,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Carson</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">"Valero Jimenez, Claudio" <<a href="mailto:claudio.valero@wur.nl" target="_blank">claudio.valero@wur.nl</a>><br>
<b>Date: </b>Monday, February 17, 2014 at 2:23 AM<br>
<b>To: </b>"<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>
<b>Subject: </b>Maker not predicting many genes<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">Dear list,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">I’m trying to annotate a fungal genome, and I’m surprised that Maker does not predict many genes (3697). I have trained SNAP and followed all the tutorials available.
Ab initio predictors are able to predict between 8000-10000 genes. It is something that I have in the configuration file that is wrong?? I attach the ops file and the SOBA summary of the annotation.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">Regards,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black">Claudio</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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