<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 thinking the same thing. Reviewing how I parse GeneMarks output, I just use their start and end coordinates (no changes). Over the weekend I altered the GeneMark parser to walk the gene start away from the supposed origin so as not to let this happen. In your E. coli test case since you have multiple contigs for what is likely a single circular genome, this would be the correct behavior as you don't want to treat each contig as an independent circular chromosome. I should probably add an is_circular option to the control files so users can select for this. I've updated the maker subversion repository so you can do an 'svn update' (I believe you are using the devel version of MAEKR correct?)</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> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Date: </span> Monday, 1 April, 2013 12:27 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Why are some start positions minus in the gff result?<br></div><div><br></div><div dir="ltr"><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><style type="text/css" id="owaParaStyle"></style><div fpstyle="1" ocsi="0"><div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi, I seem to remember some discussion of the possibility of negative coordinates in a gff3 file when the genomic material is circular. Since you're annotating viral genomes, could
this be whats happening here? Like Carson said, I've never seen this before, but that's just an idea I had.
<div><br></div><div>Daniel<br><div><br><div class="BodyFragment"><font size="2"><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></font></div></div><div style="font-family: Times New Roman; color: #000000; font-size: 16px"><hr tabindex="-1"><div id="divRpF191505" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> <a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a> [<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a>] on behalf of Hung-Wei Hsu [<a href="mailto:ares711122@gmail.com">ares711122@gmail.com</a>]<br><b>Sent:</b> Monday, March 25, 2013 8:50 PM<br><b>To:</b> <a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br><b>Subject:</b> [maker-devel] Why are some start positions minus in the gff result?<br></font><br></div><div></div><div><div dir="ltr"><span style="font-size: 14px; font-family: arial, sans-serif; ">Hi MAKER developers,</span><br><div><span style="font-size: 14px; font-family: arial, sans-serif; "><br></span></div><div style=""><span style="font-size: 14px; font-family: arial, sans-serif; ">I could successfully run MAKER and get the final gff.</span></div><div style=""><span style="font-size: 14px; font-family: arial, sans-serif; ">But I found some start positions in the gff were minus.</span></div><div style=""><span style="font-size: 14px; font-family: arial, sans-serif; ">That led to error in the gff reader.</span></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Is this a bug?</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Could you please help to resolve this problem?</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Thanks a lot in advance.</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px"><br></span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Best regards,</span></font></div><div style=""><font face="arial,sans-serif"><span style="font-size:14px">Hung-Wei</span></font></div></div></div></div></div></div></div></div>
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