<div dir="ltr">Awesome! Thanks for the tips and script. This should do the trick. Will come back if I get stuck.<div><br></div><div>Felipe</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, May 28, 2014 at 11:45 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="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>For convenience you can use the attached script to help pull out the match/match_part features you want from the GFF3 file (or you can pull them out yourself). Then do just like Daniel said by setting keep_preds=1 and giving the selected match/match_part features to pred_gf, and your current MAKER models to model_gff. </div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><div><br></div><span><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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Wednesday, May 28, 2014 at 12:35 PM<br>
<span style="font-weight:bold">To: </span> Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu" target="_blank">fbarreto@ucsd.edu</a>><br><span style="font-weight:bold">Cc: </span> MAKER group <<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] Adding non-overlapping models to final set<br></div><div><div class="h5"><div><br></div><div><div style="word-wrap:break-word">
Hi Felipe, I'm glad to hear that you got some more genes from IPRscan. If you don't care about getting the functional information from the IPRscan report and into the gff file, then you just need to pull those predictions out from all the ab-initio predictions
that you don't care about and put them in a fasta file. Then you put that file in for the "pred_gff" option and set keep_preds=1. That will promote those predictions to full gene models. Then you can merge with your other gff3 file.
<div><br></div><div>~Daniel</div><div><br></div><div><br></div><div><br><div><div><span style="font-family:Tahoma;font-size:small">Daniel Ence</span></div><div><span style="font-family:Tahoma;font-size:small">Graduate Student</span></div>
<div><a href="mailto:dence@genetics.utah.edu" target="_blank">dence@genetics.utah.edu</a><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">Eccles Institute of Human Genetics</span><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">University of Utah</span><br style="font-family:Tahoma;font-size:small"><span style="font-family:Tahoma;font-size:small">15 North 2030 East, Room 2100</span><br style="font-family:Tahoma;font-size:small">
<span style="font-family:Tahoma;font-size:small">Salt Lake City, UT 84112-5330</span></div></div><br><div><div>On May 28, 2014, at 11:39 AM, Felipe Barreto <<a href="mailto:fbarreto@ucsd.edu" target="_blank">fbarreto@ucsd.edu</a>></div>
<div> wrote:</div><br><blockquote type="cite"><div dir="ltr">Hi, all,
<div><br></div><div>I finished generating Maker gene models. Following suggestions here and from publications, I used IPRscan on the set of non-ovelapping ab initio protein models. This identified ~200 models with protein domains, and I would like to add those to my final
gene set. </div><div><br></div><div>However, I am having trouble figuring out how to use Maker's options to update my final maker_genome.gff file to include these 200 models, without also adding the remaining ~8000 non-overlapping models I don't want. The discussions about the re-annotation
options don't seem to get at this.</div><div><br></div><div>Do I have to first find a way to create a new gff file containing only the 200 new models, and then simply use gff3_merge with the full genome gff? </div>
<div><br></div><div>At this point, I am not concerned about incorporating IPRscan functional info into the gff file. I want simply to generate an updated (and final) gene set and then move on to functional annotation.</div>
<div><br></div><div><br></div><div>Thanks yet again!</div><div><br></div><div>Felipe</div><div><br clear="all"><div><br></div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br>Felipe Barreto<br>Post-doctoral Scholar<br>Scripps Institution of Oceanography<br>University of California, San Diego<br>La Jolla, CA 92093
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