<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>The consensus list is in the maker.proteins.fasta and maker.transcripts.fasta file. The predictor specific lists are just for reference purposes (incase you want to see what the other predictors produced on their own, i.e. without MAKER's intervention). The non-overlapping.fasta file in the same directory will contain consensus entries for models that were not supported by any evidence and don't overlap any gene models in the maker.transcripts.fasta (think of these as the maybe gene and the maker.transcripts.fasta as the very likely genes). You can set keep_preds=1 if you just want MAKER to keep everything with or without support and just produce consensus (probably ok on a fungus, but I wouldn't recommend it on other eukayotes because false positive rates will be very high).</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> Eduardo Larriba <<a href="mailto:larriba.ed@gmail.com">larriba.ed@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Friday, 25 May, 2012 12:01 PM<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">Subject: </span> [maker-devel] Consensus gene models<br></div><div><br></div>Hi Carson and people,<br><span id="result_box" class="" lang="en"><span class="hps">I am working on</span> <span class="hps">structural</span> <span class="hps">annotation</span> <span class="hps">of a filamentous fungus</span><span>, of which there</span> <span class="hps">is little evidence</span> <span class="hps atn"></span><span>as EST</span> <span class="hps">or</span> <span class="hps">Protein</span><span>.</span> <span class="hps">For generate </span></span><span id="result_box" class="" lang="en"><span class="hps">consensus </span></span><span id="result_box" class="" lang="en"><span class="hps">gene </span> <span class="hps">based on</span> <span class="hps">limited evidence</span>s<span class="hps"> to me</span> <span class="hps">I used</span> <span class="hps">Marker.</span><br>
<span class="hps">For this I</span> <span class="hps">created</span> <span class="hps">the files</span> <span class="hps">GeneMark</span> <span class="hps">prediction</span><span class="atn">-</span><span>is and</span> <span class="hps">SNAP.</span><br>
<span class="hps">I</span> <span class="hps">run maker </span><span class="hps">using the</span> <span class="hps">EST</span> of my organims (85)<span class="hps"></span><span class="hps"></span><span class="hps"></span><span>, along with</span> <span class="hps">5700</span> <span class="hps">EST</span> of the closed organims<span class="hps"></span><span>.</span> <span class="hps"></span>I have <span class="hps">made</span> <span class="hps">predictions with</span> <span class="hps">Augustus</span><span>,</span> <span class="hps">and</span> <span class="hps">SNAP</span> <span class="hps"></span><span class="hps"></span> <span class="hps">GeneMark, with the training files for my organims, in Maker pipeline</span><span>.</span> <span class="hps">Everything</span> <span class="hps">works fine.</span><br>
<span class="hps">My problem</span> <span class="hps">is that when</span> <span class="hps">I get</span> <span class="hps">the consensus sequences</span> <span class="hps">of all my</span> <span class="hps">contigs,</span> <span class="hps">fasta_merge</span> <span class="hps">script</span> <span class="hps">(included in</span> <span class="hps">Maker)</span><span>, I get</span> <span class="hps">different</span> <span class="hps">list for each</span> <span class="hps">predictor</span><span>, as well as</span> <span class="hps">when I try to</span> <span class="hps">get the</span> <span class="hps">gff</span> <span class="hps">of all.</span><br>
<span class="hps">They could</span> <span class="hps">tell me</span> <span class="hps">how I can use</span> <span class="hps">Maker</span> <span class="hps">consensus</span> <span class="hps">for a list</span> <span class="hps">of</span> <span class="hps">genes?</span> <span class="hps">Or I have to</span> <span class="hps">do it</span> <span class="hps">manually?</span> <span class="hps">There is</span> <span class="hps">the possibility that</span> <span class="hps">Maker</span> <span class="hps">evaluates</span> <span class="hps">the accuracy of</span> <span class="hps">each</span> <span class="hps">prediction</span> <span class="hps">and</span> <span class="hps">confirm</span><span>, so</span> <span class="hps">just get</span> <span class="hps">a list of the</span> <span class="hps">different</span> <span class="hps">predictions?</span><br><br> <span class="hps">Thank you very much</span><span>.</span></span><br><br clear="all"><br>-- <br>Eduardo Larriba Tornel<br>Universidad de Alicante.<br>Lab. Fitopatología<br>Dept. Ciencias del Mar y Biología Aplicada<br>
Pabellón 13. <br>San Vicente del Raspeig<br>Tel. 96 590 3400 ext 3280<div style="padding:0px;margin-left:0px;margin-top:0px;overflow:hidden;word-wrap:break-word;color:black;font-size:10px;text-align:left;line-height:130%"></div><div style="padding:0px;margin-left:0px;margin-top:0px;overflow:hidden;word-wrap:break-word;color:black;font-size:10px;text-align:left;line-height:130%"></div><br>
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