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Cool, thanks Brian,
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<div>Barry Moore</div>
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<div>Director, Research & Science</div>
<div>USTAR Center for Genetic Discovery</div>
<div>Dept. of Human Genetics</div>
<div>University of Utah</div>
<div>Salt Lake City, UT</div>
<div>T: (801) 858-9476</div>
<div>C: (801) 243-8819</div>
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<div>On Oct 6, 2014, at 10:02 PM, Brian Hall <<a href="mailto:bhall7@hawaii.edu">bhall7@hawaii.edu</a>> wrote:</div>
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<div bgcolor="#FFFFFF" text="#000000">Hi Barry,<br>
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Try this one:<br>
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<a class="moz-txt-link-freetext" href="http://genomeannotation.github.io/GAG/">http://genomeannotation.github.io/GAG/</a><br>
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Sorry about that!<br>
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--Brian Hall<br>
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<div class="moz-cite-prefix">On 10/06/2014 05:53 PM, Barry Moore wrote:<br>
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<blockquote cite="mid:F8BAAB7F-11B1-4367-B9FF-A2618E225405@genetics.utah.edu" type="cite">
Hi Scott,
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<div>Just FYI, github is giving me a 404 error on the link below. Were others able to follow the link successfully? </div>
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<div>B</div>
<div><br>
<div>
<div>
<div>Barry Moore</div>
<div>-------------------------------------------------</div>
<div>Director, Research & Science</div>
<div>USTAR Center for Genetic Discovery</div>
<div>Dept. of Human Genetics</div>
<div>University of Utah</div>
<div>Salt Lake City, UT</div>
<div>T: (801) 858-9476</div>
<div>C: (801) 243-8819</div>
</div>
</div>
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<div>On Apr 17, 2014, at 2:59 PM, Geib, Scott <<a moz-do-not-send="true" href="mailto:Scott.Geib@ARS.USDA.GOV">Scott.Geib@ARS.USDA.GOV</a>> wrote:</div>
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<span style="color: rgb(31, 73, 125);">Hi Brian,<o:p></o:p></span></p>
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<span style="color: rgb(31, 73, 125);">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>
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<span style="color: rgb(31, 73, 125);"><a moz-do-not-send="true" href="http://brianreallymany.github.io/GAG/" style="color: purple; text-decoration:
underline;">http://brianreallymany.github.io/GAG/</a><o:p></o:p></span></p>
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<span style="color: rgb(31, 73, 125);">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>
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<span style="color: rgb(31, 73, 125);"><br>
Scott<o:p></o:p></span></p>
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---------- Forwarded message ----------<br>
From:<span class="Apple-converted-space"> </span><b>Mack, Brian</b><span class="Apple-converted-space"> </span><<a moz-do-not-send="true" href="mailto:Brian.Mack@ars.usda.gov" style="color: purple; text-decoration: underline;">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: rgb(31, 73, 125);"> <span class="Apple-converted-space"> </span></span>" <<a moz-do-not-send="true" href="mailto:maker-devel@yandell-lab.org" style="color: purple; text-decoration: underline;">maker-devel@yandell-lab.org</a>><br>
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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 moz-do-not-send="true" href="http://gmod.827538.n3.nabble.com/NCBI-feature-table-tt4040473.html#a4040475" target="_blank" style="color: purple;
text-decoration: underline;">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></div>
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4 ERROR: SEQ_FEAT.BadTrailingCharacter<o:p></o:p></div>
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217 ERROR: SEQ_FEAT.NoStop<o:p></o:p></div>
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438 ERROR: SEQ_FEAT.ShortIntron<o:p></o:p></div>
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171 ERROR: SEQ_FEAT.StartCodon<o:p></o:p></div>
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171 ERROR: SEQ_INST.BadProteinStart<o:p></o:p></div>
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291 WARNING: SEQ_FEAT.NotSpliceConsensusAcceptor<o:p></o:p></div>
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648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor<o:p></o:p></div>
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118 WARNING: SEQ_FEAT.ShortExon<o:p></o:p></div>
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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></div>
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Thanks,<o:p></o:p></div>
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Brian<o:p></o:p></div>
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or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.<o:p></o:p></div>
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