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Hi Barry,<br>
<br>
Try this one:<br>
<br>
<a class="moz-txt-link-freetext" href="http://genomeannotation.github.io/GAG/">http://genomeannotation.github.io/GAG/</a><br>
<br>
Sorry about that!<br>
<br>
--Brian Hall<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/06/2014 05:53 PM, Barry Moore
wrote:<br>
</div>
<blockquote
cite="mid:F8BAAB7F-11B1-4367-B9FF-A2618E225405@genetics.utah.edu"
type="cite">
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Hi Scott,
<div><br>
</div>
<div>Just FYI, github is giving me a 404 error on the link below.
Were others able to follow the link successfully? </div>
<div><br>
</div>
<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>
<br>
<div>
<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>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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<p class="MsoNormal" style="margin: 0in 0in 12pt;
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<span style="color: rgb(31, 73, 125);">Hi Brian,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin: 0in 0in 12pt;
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serif;">
<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>
<p class="MsoNormal" style="margin: 0in 0in 12pt;
font-size: 12pt; font-family: 'Times New Roman',
serif;">
<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>
<p class="MsoNormal" style="margin: 0in 0in 12pt;
font-size: 12pt; font-family: 'Times New Roman',
serif;">
<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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<span style="color: rgb(31, 73, 125);"> </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>
<br>
<o:p></o:p></p>
<div>
<div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
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>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
4 ERROR: SEQ_FEAT.BadTrailingCharacter<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
217 ERROR: SEQ_FEAT.NoStop<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
438 ERROR: SEQ_FEAT.ShortIntron<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
171 ERROR: SEQ_FEAT.StartCodon<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
171 ERROR: SEQ_INST.BadProteinStart<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
291 WARNING:
SEQ_FEAT.NotSpliceConsensusAcceptor<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
648 WARNING: SEQ_FEAT.NotSpliceConsensusDonor<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
118 WARNING: SEQ_FEAT.ShortExon<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
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>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
Thanks,<o:p></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size:
12pt; font-family: 'Times New Roman', serif;">
Brian<o:p></o:p></div>
</div>
<div style="margin: 0in 0in 0.0001pt; font-size:
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<br>
<br>
<br>
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