<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 half way remember some tRNAscan bugs being fixed in several of the sub versions of 2.31 (tRNAscan was only introduced as an option in 2.30 I believe and most 2.31 updates were related to tRNAscan). Current version is 2.31.6. Could you give it a try and see if it is still giving you the issue.</div><div><br></div><div>I did a quick look through the archives and I think this was found and fixed --> <a href="https://groups.google.com/forum/#!searchin/maker-devel/trna$20strand/maker-devel/Z-kvf_V2ynU/vstSNjHgyJQJ">https://groups.google.com/forum/#!searchin/maker-devel/trna$20strand/maker-devel/Z-kvf_V2ynU/vstSNjHgyJQJ</a></div><div><br></div><div>Thanks,</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> Daniel Standage <<a href="mailto:daniel.standage@gmail.com">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, August 21, 2014 at 9:36 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<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] tRNAscan GFF3<br></div><div><br></div><div dir="ltr">This annotation was generated using Maker 2.31.3.<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>
Indiana University<br></div></div><br><br><div class="gmail_quote">On Thu, Aug 21, 2014 at 11:35 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Calibri,sans-serif"><div>It should be on the same strand. Which MAKER version are you using?</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span><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 Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, August 21, 2014 at 9:33 AM<br><span style="font-weight:bold">To: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] tRNAscan GFF3<br></div><div><div class="h5"><div><br></div><div dir="ltr"><div><div>Greetings!<br><br>I have a quick question about Maker's handling of tRNAscan output, particularly tRNAs containing introns. If I haven't missed something, it looks like Maker reports the second exon on the opposite strand as the first exon, the tRNA feature, and the gene feature? Am I reading this correctly?<br><br></div>I don't think this representation makes sense. The second exon is complementary to the first (hence the folding), but it is not encoded on or transcribed from the opposite strand. Unless I've misunderstood something, I would suggest that the correct representation would be to have all features on the same strand.<br><br></div>Thanks,<br>Daniel<br clear="all"><div><div><div><div><div dir="ltr"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Computational Genome Science Laboratory<br>Indiana University<br></div></div></div></div></div></div></div></div>
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