<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>I'm sorry I don’t' understand question 1. You are you missing resulting fasta files, correct? Did your resulting GFF3 file have any features of type "gene"? Did you run fasta_merge after running gff3_merge?</div><div><br></div><div>Could you give me more details on what you are trying to do, so I can take a stab at question 2 as well.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> Diana LeDuc <<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>><br><span style="font-weight:bold">Reply-To: </span> Diana LeDuc <<a href="mailto:diana_leduc@eva.mpg.de">diana_leduc@eva.mpg.de</a>><br><span style="font-weight:bold">Date: </span> Friday, 10 May, 2013 10:44 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Cc: </span> Gabriel Renaud <<a href="mailto:gabriel_renaud@eva.mpg.de">gabriel_renaud@eva.mpg.de</a>>, Janet Kelso <<a href="mailto:kelso@eva.mpg.de">kelso@eva.mpg.de</a>>, Torsten Schoeneberg <<a href="mailto:torsten.schoeneberg@medizin.uni-leipzig.de">torsten.schoeneberg@medizin.uni-leipzig.de</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Maker consensus<br></div><div><br></div><div xmlns="http://www.w3.org/1999/xhtml">
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<p>Dear maker developers,</p>
<p>I am a phD student working on de novo assembly and annotation of a bird genome. I used Maker as annotation pipeline, which ran very well, and I obtained different annotations with evidence from Augustus gene predictor, small EST dataset from my organism and protein sequences from chicken, turkey and zebrafinch. I could combine the different gff files from different scaffolds into one gff file with annotations for the entire genome.</p>
<p>I now have two questions:</p>
<p>1. What could be the reason that I haven't gotten the protein.fasta and trancript.fasta files</p>
<p>2. How can I obtain a consensus gene list of different evidences from maker? What I would actually need is the scaffold, coordinates and annotation (gene name) according to the 3 other bird species.</p> Thank you in advance.
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Best regards,
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Diana Le Duc
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--
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<br>Max Planck Institute for Evolutionary Anthropology
<br>Department of Evolutionary Genetics
<br>Deutscher Platz 6
<br>D-04103 Leipzig
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<br>Phone +49 (0)341-3550-554
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<a target="_blank" href="http://www.eva.mpg.de">www.eva.mpg.de</a>
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