<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>Very cool. I'll try it out as well.</div><div><br></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> "Geib, Scott" <<a href="mailto:Scott.Geib@ARS.USDA.GOV">Scott.Geib@ARS.USDA.GOV</a>><br><span style="font-weight:bold">Date: </span> Thursday, April 17, 2014 at 2:59 PM<br><span style="font-weight:bold">To: </span> "Mack, Brian" <<a href="mailto:Brian.Mack@ARS.USDA.GOV">Brian.Mack@ARS.USDA.GOV</a>>, "<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>>, "Brian Hall (<a href="mailto:bhall7@hawaii.edu">bhall7@hawaii.edu</a>)" <<a href="mailto:bhall7@hawaii.edu">bhall7@hawaii.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] tbl2asn errors<br></div><div><br></div><div xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="Generator" content="Microsoft Word 15 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--><div lang="EN-US" link="blue" vlink="purple"><div class="WordSection1"><div><div><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D">Hi Brian,
<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D">We have a tool to deal with this in development, you should not directly upload your maker output to NCBI, you need to filter out genes, check that things are sane, etc.
<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D"><a href="http://brianreallymany.github.io/GAG/">http://brianreallymany.github.io/GAG/</a><o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D">It is still in active development, first full release is planned for the end of this month (if you can wait 1.5 weeks). It has no dependencies and maintains parent/child relationships
(for example if you remove a gene, it will also remove associated CDS/mRNA). In a release planned for then end of the month, you will be able to perform functions like removing short features, long features, flagging things for review, etc. It also generates
an updated genome.fasta file, gff3 file, and sequences files for CDS/mRNA/peptide based on edits made. Hopefully this is helpful to you.<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D"><br>
Scott<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#1F497D"><o:p> </o:p></span></p><p class="MsoNormal" style="margin-bottom:12.0pt">---------- Forwarded message ----------<br>
From: <b>Mack, Brian</b> <<a href="mailto:Brian.Mack@ars.usda.gov">Brian.Mack@ars.usda.gov</a>><br>
Date: Thu, Apr 17, 2014 at 10:34 AM<br>
Subject: [maker-devel] tbl2asn errors<br>
To: "<span style="color:#1F497D"> </span><a href="mailto:maker-devel@yandell-lab.org"></a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><br><o:p></o:p></p><div><div><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi, I thought I would try asking my question here as NCBI was not able to give me much assistance. In preparation for submitting to NCBI, I converted my my MAKER gff3 to NCBI tbl
format using the gff32tbl script that Carson posted a link to in this thread (<a href="http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475" target="_blank">http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475</a>).
It seemed to have converted fine, however when I use NCBIs tbl2asn program I get numerous errors in my errorsummary.val file:<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 4 ERROR: SEQ_FEAT.BadTrailingCharacter<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 217 ERROR: SEQ_FEAT.NoStop<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 438 ERROR: SEQ_FEAT.ShortIntron<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 171 ERROR: SEQ_FEAT.StartCodon<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 171 ERROR: SEQ_INST.BadProteinStart<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> 118 WARNING: SEQ_FEAT.ShortExon<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">In addition, all of the genes, cds, and mRNA coordinates in the resulting sqn files are decreased by one. For example my tbl file will have gene coordinates of 440869 – 441931,
but the sqn file will have 440868 – 441930. Any ideas what might be causing this?<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p><p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Brian<o:p></o:p></p></div><p class="MsoNormal"><br><br><br><br>
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<o:p></o:p></p></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>
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