<div dir="ltr">I appreciate the feedback. I will try letting MAKER run augustus instead of passing the Augustus predictions as GFF3. <div><br></div><div style>Thanks for all you help!</div><div style><br></div><div style>Getiria</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jun 7, 2013 at 5:10 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<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>You seem to be running this in a very odd way. First the GFF3 is not correctly formatted. There are lines containing score=1 (all by itself)? I believe this may be coming through because you are trying to pass in augustus predictions as GFF3 and that input is malformed. All of your Augustus models are also single exon genes, but they are very long and do not even correspond to proper ORFs. The EST evidence is spliced and is thus contradicting the augustus model (they don't support each other). If you want MAKER to be able to use the evidence as feedback for the model, you need to let MAKER run augustus. Otherwise it is only able to accept or reject the model from the GFF3 (nothing more – no attempt at consensus).</div>
<div><br></div><div>Perhaps if you supply you input dataset and control files we can help you get the best settings. You would need to provide the Augustus species set you are using as well (contained in a directory in …/augustus/config/species).</div>
<div><br></div><div>--Carson</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> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Friday, 7 June, 2013 2:08 PM<div>
<div class="h5"><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><br>
<span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: accessory scripts<br></div></div></div><div><div class="h5"><div><br></div><div dir="ltr"><p style="margin:0px;font-size:14px;font-family:Menlo;color:rgb(42,53,214)">
<span style="color:rgb(34,34,34);font-family:Calibri,sans-serif">Carson, </span></p><p style="margin:0px"><font face="Calibri,sans-serif"><span style="font-size:14px">I have attached the full gff3 for the contig together with a screen shot from IGV with regions I was expecting Maker to make a consensus call. The region on question is </span></font><span style="font-size:18px;font-family:Menlo">CGS00003:</span><span style="color:rgb(42,53,214);font-family:Menlo;font-size:14px">5264784</span><span style="font-size:18px;font-family:Menlo">-</span><span style="color:rgb(42,53,214);font-family:Menlo;font-size:14px">5273457. </span><span style="font-size:14px;font-family:Calibri,sans-serif">I will greatly appreciate any insights. </span></p>
<p style="margin:0px"><span style="font-size:14px;font-family:Calibri,sans-serif"><br></span></p><p style="margin:0px"><span style="font-size:14px;font-family:Calibri,sans-serif">Thanks, </span></p><p style="margin:0px"><span style="font-size:14px;font-family:Calibri,sans-serif">Getiria </span></p>
<p style="margin:0px;font-size:14px;font-family:Menlo;color:rgb(42,53,214)"><br></p></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jun 6, 2013 at 8:55 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<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 thing to keep in mind is the strandedness of the evidence and the model (they must be on the same strand). Further protein evidence is only valid support if it is in the same reading frame as the model.</div>
<div><br></div><div>Could you send the full GFF3 for the contig (I need features and GFF3 internal fasta) and the coordinates of the region in question, and I can take a look? Also if you can, it would be good to let maker run Augustus as well with the species file rather than just passing in the GFF3. This is because MAKER can only talk to Augustus to generate competing hint based models if you provide the species.</div>
<div><br></div><div>Thanks,</div><div>Carson</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> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 1:10 PM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><div>
<div><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: accessory scripts<br></div></div></div><div><div><div><br></div><div dir="ltr">I checked visually in IGV and there are some exons in the predicted model with protein and EST support but the maker output GFF only has match_part and protein_match in column 3. Does that mean Maker doesn't deem any of the evidence sufficient to make a gene model prediction? <div>
<br></div><div>I guess I am somewhat surprised I am not getting any exons predicted by Maker. Is there a parameter I can alter to reduce the threshold at which Maker makes this call? I have attached the first 400 lines of one of my GFF files together with the control file (maker_opts.ctl) just in case they might be useful. </div>
<div><br></div><div>Getiria </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 5, 2013 at 9:47 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<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>Also, just a note, models are rejected if they have no protein or EST support. This is because ab inito predictors over predict (you may have 10 false positives for every true positive in some genomes for example).</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> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 10:44 AM<br>
<span style="font-weight:bold">To: </span> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>>, Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><div>
<br><span style="font-weight:bold">Cc: </span> "<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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><br>
</div><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker: accessory scripts<br></div><div><div><div><br></div><div><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>
All maker gene annotations will be of the format gene/mRNA/exon/CDS. Anything in the format match/match_part is an evidence alignment or rejected model and is there for reference purposes. If you want to upgrade all of the rejected loci to gene annotations, set keep_preds=1 in the control files. If you want to upgrade a subset of rejected models to a full annotation, create a list of IDs (one per line) then give them to the attached script. gff3_preds2models was previously deprecated and no longer part of the maker distribution, but the attached script is an updated version with the same functionality. </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> Innocent Onsongo <<a href="mailto:onson001@umn.edu" target="_blank">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 5 June, 2013 12:35 PM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carson.holt@oicr.on.ca" target="_blank">carson.holt@oicr.on.ca</a>><br><span style="font-weight:bold">Cc: </span> "<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>>, Barry Moore <<a href="mailto:barry.utah@gmail.com" target="_blank">barry.utah@gmail.com</a>><br>
<span style="font-weight:bold">Subject: </span> [maker-devel] Maker: accessory scripts<br></div><div><br></div><div dir="ltr">I was able to successfully ran Maker and now want to c<span style="line-height:19px;font-size:13px;font-family:sans-serif">onverts the gene prediction match/match_part format to annotation gene/mRNA/exon/CDS format. I looked at the tutorial and the script </span><span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace">gff3_preds2models</span><div>
<span style="line-height:19px;font-size:13px;font-family:sans-serif">is supposed to do this conversion. How do I access this script. It is not in </span>/maker/2.28-beta/bin/<br></div><div><br></div><div>Also, in running <span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace">gff3_preds2models <gff3 file> <pred list> </span> is <<span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace">pred list> the file I used for </span><span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace">pred_gff=? </span></div>
<div><span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace"><br></span></div><div>Long story short, how do I transform the GFF output from Maker to the more traditional annotation of exon/intron? <br>
</div><div><br></div><div><span style="line-height:19px;font-size:13px;background-color:rgb(249,249,249);font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace">Thanks, </span></div><div>Getiria</div>
</div>
_______________________________________________
maker-devel mailing list
<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></span></div>
</div></div></div></span></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: <a href="tel:612-624-0532" value="+16126240532" target="_blank">612-624-0532</a></div></div></div></span></div></blockquote></div><br><br clear="all"><div><br></div>
-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: <a href="tel:612-624-0532" value="+16126240532" target="_blank">612-624-0532</a>
</div></div></div></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: 612-624-0532
</div>