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On a somewhat related note, is there an advantage of using BUSCO
to train Augustus instead of the provided Augustus webtraining
service? Does anybody know how those 2 compare?<br>
<br>
<br>
Am 13.05.2016 um 09:56 schrieb Panos Ioannidis:<br>
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<div dir="ltr">Hello Ian,
<div><br>
</div>
<div>Xabier is right. You have to run BUSCO with the <font
face="monospace, monospace">--long</font> switch and then,
in the <font face="monospace, monospace">maker_opts.ctl</font> file,
you should point the <font face="monospace, monospace">augustus_species</font> variable
to your trained species (i.e. the name you pass with the <font
face="monospace, monospace">-o/-a</font> parameter).</div>
<div><br>
</div>
<div>So, in Xabier's example your <font face="monospace,
monospace">maker_opts.ctl</font> file should contain the
following line:</div>
<div><br>
</div>
<div><font face="monospace, monospace">augustus_species=Genus_species</font></div>
<div><font face="monospace, monospace"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Felipe, Rob, is
there something else that I'm missing? Truth is that I
haven't run this recently and there might be differences in
newer BUSCO versions.</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><span style="font-family:arial,helvetica,sans-serif">Panos</span><br>
</div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Panos Ioannidis,
PhD</font></div>
<div><font face="arial, helvetica, sans-serif">Postdoctoral
researcher</font></div>
<div><font face="arial, helvetica, sans-serif">Computational
Evolutionary Genomics Group</font></div>
<div><font face="arial, helvetica, sans-serif">University of
Geneva</font></div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, May 13, 2016 at 2:31 AM,
Xabier Vázquez Campos <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:xvazquezc@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:xvazquezc@gmail.com">xvazquezc@gmail.com</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Check this thread:<br>
<a moz-do-not-send="true"
href="https://groups.google.com/forum/#%21topic/maker-devel/vp8R06VVQGQ"
target="_blank">https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ</a><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">
<div>
<div>On 26 April 2016 at 02:20, Misner, Ian
(NIH/NIAID) [C] <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:ian.misner@nih.gov"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:ian.misner@nih.gov">ian.misner@nih.gov</a></a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
<div
style="word-wrap:break-word;color:rgb(0,0,0);font-size:14px;font-family:Garamond,sans-serif">
<div>Hello,</div>
<div><br>
</div>
<div>Are there any guidelines for using BUSCO
to help train MAKER? CEGMA has been
discontinued but I used to use the <a
moz-do-not-send="true"
href="http://cegma2zff.pl" target="_blank">cegma2zff.pl</a>
steps to use those proteins as a training
step. BUSCO seems to train Augustus but I'm
not sure what file to pass from BUSCO to
MAKER for this to be properly utilized. I
didn't see anything specific about this in
the archives. </div>
<div>
<div>-----</div>
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-- <br>
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<div>Xabier Vázquez-Campos, <i>PhD</i><br>
<i>Research Associate</i><br>
Water Research Centre<br>
School of Civil and Environmental
Engineering<br>
The University of New South Wales<br>
Sydney NSW 2052 AUSTRALIA<br>
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