<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>Yes the advice given so far is correct. You can pass back through old evidence using the maker_gff option and setting est_pass, protein_pass, etc. to 1. Set the pred_pass=0 so as to ignore old predictions. Let MAKER generate those again to reflect the additional evidence (added to the alt_est= option). If you have model_pass=1 and map_forward=1 set then if any model changes, you can at least maintain the name.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Jason Stajich <<a href="mailto:jason.stajich@gmail.com">jason.stajich@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Sunday, 17 June, 2012 12:30 AM<br><span style="font-weight:bold">To: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<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] Quick question about re-annotation<br></div><div><br></div>Well remember that ESTs are used as extra helper information to the ab initio gene predictors so it will want to run all those predictions again and re-call the gene structures from the combined output with this extra info added in. So you will need to decide how you want these to be incorporated and if you are willing to wait for the analysis to complete again with this info. The pass through of the previous run will allow you to keep the names from that previous run if they are important to you.<div><br><div>Jason Stajich<br><br><br><div class="gmail_quote">On Thu, Jun 14, 2012 at 7:48 PM, Gowthaman Ramasamy <span dir="ltr"><<a href="mailto:gowthaman.ramasamy@seattlebiomed.org" target="_blank">gowthaman.ramasamy@seattlebiomed.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Of course, Carson knows the best answer.<br><br>
But, I think, you need to grab the GFFs from your previous maker run, and pass it as model_gff= option. That way, gene models in GFFs are used as a starting point and now will check for evidences from your alt_est dataset....<br><br>
-Gowthaman<br>
________________________________________<br>
From: <a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a> [<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] On Behalf Of Daniel Standage [<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>]<br>
Sent: Thursday, June 14, 2012 11:26 AM<br>
To: Maker Mailing List<br>
Subject: [maker-devel] Quick question about re-annotation<br><div><div class="h5"><br>
Greetings!<br><br>
I have a quick question about re-annotation with Maker. I have successfully completed a Maker run, but now I would like to re-run Maker with some additional EST evidence (from a related organism, aligned and in GFF3 format). I simply added the file to the altest_gff configuration setting and re-ran Maker. However, from the log messages it looked like Maker was starting from scratch rather than using what had already been completed in the initial run. Luckily, I had made a backup of the complete Maker data structure, so I killed the job, deleted the data structure, and restored from the backup.<br><br>
Before I try to run this again, do I need to change any other configuration settings to do this re-annotation? The stanza under Re-annotation Using MAKER Derived GFF3 looks relevant, but it is not clear to me which settings need to be set.<br><br>
Thanks!<br><br>
--<br>
Daniel S. Standage<br>
Ph.D. Candidate<br>
Bioinformatics and Computational Biology Program<br>
Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br><br><br></div></div>_______________________________________________<br>
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