<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">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/#!topic/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">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>
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<div>Hello,</div>
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<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>
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<br></blockquote></div><span><font color="#888888"><br><br clear="all"><br>-- <br><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Xabier Vázquez-Campos, <i>PhD</i><br><i>Research Associate</i><br>Water Research Centre<br>School of Civil and Environmental Engineering<br>
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