<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>This might be a round about way to get them to have the names unaltered. Give the pred_gff ones to est_gff. Still give the model_gff ones to model_gff. Set est2genome=1 and single_exon=1. Then add this line to the control file est_forward=1. This is normally used to move transcripts forward onto new assemblies with names being drawn from the alignment, but by telling MAKER that these are ESTs instead of predictions and setting the appropriate values, it will think it's moving transcripts forward, and the final result may be what you want.</div><div><br></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> Anthony Bretaudeau <<a href="mailto:anthony.bretaudeau@rennes.inra.fr">anthony.bretaudeau@rennes.inra.fr</a>><br><span style="font-weight:bold">Date: </span> Thursday, June 12, 2014 at 10:17 AM<br><span style="font-weight:bold">To: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Cc: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</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] Merging 2 annotations<br></div><div><br></div><div>
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Yes, I think that's why the ids get changed.<br>
But I don't know which predictions I want to keep as I'm using maker
to only keep the ones that are not equivalent to the models that are
in the model_gff.<br>
<br>
Anthony<br>
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<div class="moz-cite-prefix">On 12/06/2014 17:50, Daniel Ence wrote:<br>
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Hi Anthony, So I think that the gene ID gets changed in the
process of promoting things from pred_gff to gene models. If you
know which predictions you want to keep, then you can select those
out and pass them to model_gff.
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<div>~Daniel</div>
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<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 moz-do-not-send="true" href="mailto:dence@genetics.utah.edu">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>
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<br>
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<div>On Jun 12, 2014, at 7:00 AM, Anthony Bretaudeau <<a moz-do-not-send="true" href="mailto:anthony.bretaudeau@rennes.inra.fr">anthony.bretaudeau@rennes.inra.fr</a>></div>
<div> wrote:</div>
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<blockquote type="cite"><span style="font-family: Helvetica;
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normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; display: inline !important; float: none; ">A little
question which is related: I set the map_forward option to
1, but it seems to work only for the model_gff gff. Is
there a way to make it keep the original IDs also for the
pred_gff file?</span><br style="font-family: Helvetica;
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