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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Innocent, I'm just jumping in this conversation kind of late in the game, but if you look in the gff3 file that maker gave you, do you see any gene, exon, or CDS features in
the output? When you give evidence (protein or EST) and ab-initio predictors to maker the default behavior is to create gene models.
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<div><span style="font-size: 10pt;">Thanks,</span></div>
<div>Daniel<br>
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<div class="PlainText">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</div>
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<div id="divRpF133082" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> maker-devel-bounces@yandell-lab.org [maker-devel-bounces@yandell-lab.org] on behalf of Innocent Onsongo [onson001@umn.edu]<br>
<b>Sent:</b> Wednesday, June 05, 2013 10:35 AM<br>
<b>To:</b> Carson Holt<br>
<b>Cc:</b> maker-devel@yandell-lab.org; Barry Moore<br>
<b>Subject:</b> [maker-devel] Maker: accessory scripts<br>
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<div dir="ltr">I was able to successfully ran Maker and now want to c<span style="color:rgb(0,0,0); font-family:sans-serif; font-size:13px; line-height:19px">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="background-color:rgb(249,249,249); color:rgb(0,0,0); font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace; font-size:13px; line-height:19px">gff3_preds2models</span>
<div style=""><span style="color:rgb(0,0,0); font-family:sans-serif; font-size:13px; line-height:19px">is supposed to do this conversion. How do I access this script. It is not in </span>/maker/2.28-beta/bin/<br>
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<div style="">Also, in running <span style="background-color:rgb(249,249,249); color:rgb(0,0,0); font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace; font-size:13px; line-height:19px">gff3_preds2models <gff3 file> <pred list> </span> is <<span style="background-color:rgb(249,249,249); color:rgb(0,0,0); font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace; font-size:13px; line-height:19px">pred
list> the file I used for </span><span style="background-color:rgb(249,249,249); color:rgb(0,0,0); font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace; font-size:13px; line-height:19px">pred_gff=? </span></div>
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<div style="">Long story short, how do I transform the GFF output from Maker to the more traditional annotation of exon/intron? <br>
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<div style=""><span style="background-color:rgb(249,249,249); color:rgb(0,0,0); font-family:'Lucida Console',Monaco,'Courier New',Courier,monospace; font-size:13px; line-height:19px">Thanks, </span></div>
<div style="">Getiria</div>
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