<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>Not something I've seen before, but there was a patch for another issue that was cause by the use of avoid_est_fusion=1, that may be related. Try the current stable release 2.31, and let me know if it still happens.</div><div><br></div><div>You can also upload the contig folder from one of the regions in question here --> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div><br></div><div>Then I could verify the bug, and see if it is something that happens in the current release.</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> Benjamin Rubin <<a href="mailto:brubin@fieldmuseum.org">brubin@fieldmuseum.org</a>><br><span style="font-weight:bold">Date: </span> Saturday, March 29, 2014 at 10:24 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] Missing UTRs in GFF<br></div><div><br></div><div dir="ltr">I have annotated a eukaryotic genome with MAKER 2.30. I recently realized that there are a few genes in the GFF file produced by gff3_merge with inconsistencies in the annotated CDS and UTRs. For most of my genes, the UTRs have their own lines in the GFF file. However, for the problematic genes, the UTRs are not specified in the GFF file and all exons are annotated as CDS. The UTRs do appear in the gene header and the protein sequences are the correct length (do not include the UTR). I have attached an example from the GFF file. <div><br></div><div>Is this a known problem, or have I done something wrong? Is there an easy way to fix the GFF file? </div><div><br></div><div>Thanks for your help,</div><div>Ben<br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">_____________________________________________________<br>Benjamin ER Rubin</span><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">PhD Candidate</span><div><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><span style="border-collapse:separate;font-family:arial;font-size:small"><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Committee on Evolutionary Biology</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">University of Chicago</span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><a href="http://benrubin.org" target="_blank"><font color="#0658b5">b</font>enrubin.org</a></span></div></span></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;"><br></span></div><div><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;">Division of Insects<br>
Zoology Department<br>Field Museum of Natural History<br>1400 South Lake Shore Drive<br>Chicago, IL 60605<br>USA<br>Office: (312) 665-7776</span></div></div></div></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></body></html>