<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 option in trinity is --jaccard_clip</div><div>--> <a href="http://trinityrnaseq.sourceforge.net/#jaccard_clip">http://trinityrnaseq.sourceforge.net/#jaccard_clip</a></div><div><br></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> Innocent Onsongo <<a href="mailto:onson001@umn.edu">onson001@umn.edu</a>><br><span style="font-weight:bold">Date: </span> Tuesday, 21 May, 2013 11:58 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">Subject: </span> [maker-devel] Maker: Re-annotation<br></div><div><br></div><div dir="ltr">Maker Development Team, <div><br></div><div>I am trying to use Maker for re-annotation using gene predictions from Augustus. We had previously used Augustus for gene prediction but now want to combine these annotations with some EST data. I updated fields maker_opts.ctl as below</div><div><br></div><div>genome=CGS01058.fasta #genome sequence file in fasta format</div><div>est_gff=EST2Scaffold.gff3 # ESTs mapped to CGS01058.fasta using BLAT</div><div>pred_gff=Augustus.gff3 #ab-initio predictions from<br></div><div><div>other_gff=Promoters.gff3 #promoter annotations</div><div>other_gff=CpG_Islands.gff3 # CpG island annotations</div></div><div><br></div><div style="">Maker runs to completion and according to the log file annotation was successful. However, it also gives a "Segmentation fault (core dumped)" message. It does produce a GFF3 file but when I load the GFF3 file into IGV and look it does not contain any of the exon definitions in Augustus.gff3. Am I missing something? </div><div style=""><br></div><div style="">Regards, </div><div style="">Getiria</div><div><div><br></div>-- <br>Getiria Onsongo, Ph.D.<br>Informatics Analyst, Research Informatics Support System<br>Minnesota Supercomputing Institute for Advanced Computational Research<br>
University of Minnesota<br>Minneapolis, MN 55455<br>Phone: 612-624-0532
</div></div>
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