<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>Do you have a small test contig I could use to duplicate the error? That will make it easier to fix.</div><div><br></div><div>Thanks,</div><div>Carson</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> Jacques Dainat <<a href="mailto:jacques.dainat@imbim.uu.se">jacques.dainat@imbim.uu.se</a>><br><span style="font-weight:bold">Date: </span> Friday, May 23, 2014 at 1:56 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] Possible error in tRNA annotation by maker<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Hi,</div><div>I would like to submit a possible error that occurs by using the tRNA annotation by maker.</div><div>I saw the problem in the gff result file. The problem occurs in <u>only</u> and for all the tRNA who have an intron and that are in the + strand. Indeed, in this case the strand of one of the exon seems to be wrong (see the example below).</div><div><br></div><div>As exemple we have:</div><div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);">scaffold6501<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>2126<span class="Apple-tab-span" style="white-space:pre"> </span>2230<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); position: static; z-index: auto;">scaffold6501<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>tRNA<span class="Apple-tab-span" style="white-space:pre"> </span>2126<span class="Apple-tab-span" style="white-space:pre"> </span>2230<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); position: static; z-index: auto;">scaffold6501<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>2185<span class="Apple-tab-span" style="white-space:pre"> </span>2230<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);">scaffold6501<span class="Apple-tab-span" style="white-space:pre"> </span>maker<span class="Apple-tab-span" style="white-space:pre"> </span>exon<span class="Apple-tab-span" style="white-space:pre"> </span>2126<span class="Apple-tab-span" style="white-space:pre"> </span>2163<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>XXX</div></div><div><br></div><div>Theoretically, we should obtain:</div><div><div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);">scaffold6501<span class="Apple-tab-span" style="white-space: pre;"> </span>maker<span class="Apple-tab-span" style="white-space: pre;"> </span>gene<span class="Apple-tab-span" style="white-space: pre;"> </span>2126<span class="Apple-tab-span" style="white-space: pre;"> </span>2230<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>+<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); position: static; z-index: auto;">scaffold6501<span class="Apple-tab-span" style="white-space: pre;"> </span>maker<span class="Apple-tab-span" style="white-space: pre;"> </span>tRNA<span class="Apple-tab-span" style="white-space: pre;"> </span>2126<span class="Apple-tab-span" style="white-space: pre;"> </span>2230<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>+<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0); position: static; z-index: auto;">scaffold6501<span class="Apple-tab-span" style="white-space: pre;"> </span>maker<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>2126<span class="Apple-tab-span" style="white-space: pre;"> </span>2163<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>+<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>XXX</div><div style="margin: 0px; font-size: 13px; font-family: 'Lucida Console'; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);">scaffold6501<span class="Apple-tab-span" style="white-space: pre;"> </span>maker<span class="Apple-tab-span" style="white-space: pre;"> </span>exon<span class="Apple-tab-span" style="white-space: pre;"> </span>2185<span class="Apple-tab-span" style="white-space: pre;"> </span>2230<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>+<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;"> </span>XXX</div></div></div><div><br></div><div>kind regards,</div><br><div apple-content-edited="true"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div>Jacques Dainat, PhD</div><div>BILS (Bioinformatics Infrastructure for Life Sciences)</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Adress: (room E10:3312)</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Uppsala University, BMC<br>Department of Medical Biochemistry Microbiology, Genomics</div>Husargatan 3, box 582</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">S-75123 Uppsala Sweden</div></div></div></div></div></div><br></div></div>_______________________________________________
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