<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif">I would guess that the main 'advantage' of using BUSCO to train Augustus is that one will probably run BUSCO on one's genome anyway before starting MAKER, so there will already be a useful set of trained parameters ready to use. I guess the 'advantage' of using the Augustus webtraining service is that one could give it much more starting data (if indeed this is available, e.g. cDNAs). Indeed if there was enough time and it made a substantial difference one might even use the BUSCO gene model output as the 'Training gene structure file' for Augustus webtraining service. I don't believe that anyone has done a comparison on how different the trained parameters end up being.</div><div class="gmail_default" style="font-family:verdana,sans-serif"><br></div><div class="gmail_default" style="font-family:verdana,sans-serif">Rob</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><br></div><div> \\ Dr Robert Waterhouse</div><div>O0o-- SIB maître assistant</div><div> "" <a href="http://www.rmwaterhouse.org" target="_blank">www.rmwaterhouse.org</a></div><div><br></div><div>A maturing understanding of the composition of the insect gene repertoire <a href="http://www.sciencedirect.com/science/article/pii/S2214574515000073" target="_blank">COIS 2015</a><br></div><div>BUSCO: assessing genome assembly and annotation completeness <a href="http://bioinformatics.oxfordjournals.org/content/early/2015/06/27/bioinformatics.btv351.full" target="_blank">Bioinformatics 2015</a><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 13 May 2016 at 12:14, Dolze, Florian <span dir="ltr"><<a href="mailto:fdolze@students.uni-mainz.de" target="_blank">fdolze@students.uni-mainz.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div><br>
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?<div><div class="h5"><br>
<br>
<br>
Am 13.05.2016 um 09:56 schrieb Panos Ioannidis:<br>
</div></div></div>
<blockquote type="cite"><div><div class="h5">
<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 href="mailto:xvazquezc@gmail.com" target="_blank"></a><a href="mailto:xvazquezc@gmail.com" target="_blank">xvazquezc@gmail.com</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 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 href="mailto:ian.misner@nih.gov" target="_blank"></a><a href="mailto:ian.misner@nih.gov" target="_blank">ian.misner@nih.gov</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 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>
-- <br>
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<div dir="ltr">
<div>Xabier Vázquez-Campos, <i>PhD</i><br>
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Water Research Centre<br>
School of Civil and Environmental
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