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<div class="">Our group have mainly used the BUSCO model in the ‘bootstrap’ run for MAKER, then retrain Augustus and SNAP using a filtered data set from that run for new rounds of MAKER.</div>
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<div class="">Also, one personal observation: we have found some genome assemblies where BUSCO performs poorly compared to CEGMA (e.g. BUSCO reports poor overall percent of SCO present, while CEGMA reports much higher numbers). We’re still delving into this,
but in those cases we avoid using the BUSCO model for obvious reasons.</div>
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<div class="">chris</div>
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<div class="">On May 13, 2016, at 3:28 AM, Robert Waterhouse <<a href="mailto:robert.waterhouse@gmail.com" class="">robert.waterhouse@gmail.com</a>> wrote:</div>
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<div class="gmail_default" style="font-family: verdana, sans-serif;">I think in the Augustus 'species' directory there should be a new folder named according to your BUSCO run, and in that folder should be the trained parameters for your new species, so from
MAKER I guess you can point to these trained parameters.</div>
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<div class="gmail_default" style="font-family: verdana, sans-serif;">Rob</div>
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<div class=""> \\ Dr Robert Waterhouse</div>
<div class="">O0o-- SIB maître assistant</div>
<div class=""> "" <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rmwaterhouse.org&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=PkOj8WcuzTUkJSiOyd8PckeY6jDwgXIaGHLfxRpM_jQ&e=" target="_blank" class="">www.rmwaterhouse.org</a></div>
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<div class="">A maturing understanding of the composition of the insect gene repertoire<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sciencedirect.com_science_article_pii_S2214574515000073&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=bQEtPdLzzK-aA_CU1jUsGJSpOVJj1L8KQPqEy3Y3ryk&e=" target="_blank" class="">COIS
2015</a><br class="">
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<div class="">BUSCO: assessing genome assembly and annotation completeness<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinformatics.oxfordjournals.org_content_early_2015_06_27_bioinformatics.btv351.full&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=QUFAzNyvgTS2NMA6NvMruQWvuH7WVrkJbdqiwBD5QvA&e=" target="_blank" class="">Bioinformatics
2015</a><br class="">
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<div class="gmail_quote">On 13 May 2016 at 09:56, Panos Ioannidis<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:panos.ioannidis@gmail.com" target="_blank" class="">panos.ioannidis@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div dir="ltr" class="">Hello Ian,
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<div class="">Xabier is right. You have to run BUSCO with the<span class="Apple-converted-space"> </span><font face="monospace, monospace" class="">--long</font><span class="Apple-converted-space"> </span>switch and then, in the<span class="Apple-converted-space"> </span><font face="monospace, monospace" class="">maker_opts.ctl</font> file,
you should point the<span class="Apple-converted-space"> </span><font face="monospace, monospace" class="">augustus_species</font> variable to your trained species (i.e. the name you pass with the<span class="Apple-converted-space"> </span><font face="monospace, monospace" class="">-o/-a</font><span class="Apple-converted-space"> </span>parameter).</div>
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<div class="">So, in Xabier's example your<span class="Apple-converted-space"> </span><font face="monospace, monospace" class="">maker_opts.ctl</font><span class="Apple-converted-space"> </span>file should contain the following line:</div>
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<div class=""><font face="monospace, monospace" class="">augustus_species=Genus_species</font></div>
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<div class=""><font face="arial, helvetica, sans-serif" class="">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>
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<div class=""><span style="font-family: arial, helvetica, sans-serif;" class="">Panos</span><br class="">
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<div class=""><font face="arial, helvetica, sans-serif" class="">Panos Ioannidis, PhD</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Postdoctoral researcher</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">Computational Evolutionary Genomics Group</font></div>
<div class=""><font face="arial, helvetica, sans-serif" class="">University of Geneva</font></div>
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<div class="gmail_quote">On Fri, May 13, 2016 at 2:31 AM, Xabier Vázquez Campos<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:xvazquezc@gmail.com" target="_blank" class="">xvazquezc@gmail.com</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div dir="ltr" class="">Check this thread:<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_forum_-23-21topic_maker-2Ddevel_vp8R06VVQGQ&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=LOPsrMMxPBDmfBDJTBpsLGpYd7_pecEb7rxNXO-oOnw&e=" target="_blank" class="">https://groups.google.com/forum/#!topic/maker-devel/vp8R06VVQGQ</a><br class="">
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<div class="">On 26 April 2016 at 02:20, Misner, Ian (NIH/NIAID) [C]<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:ian.misner@nih.gov" target="_blank" class="">ian.misner@nih.gov</a>></span><span class="Apple-converted-space"> </span>wrote:<br class="">
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<div class="">Hello,</div>
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<div class="">Are there any guidelines for using BUSCO to help train MAKER? CEGMA has been discontinued but I used to use the<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__cegma2zff.pl&d=CwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=jK3HLznqS7mlwXNI4FHO3K_o5EX29RgO9ccngyj7Dzg&s=R1NsitSMN4RwzwYuaNjszxmyBogW6wSOa8NWl4Sny_k&e=" target="_blank" class="">cegma2zff.pl</a><span class="Apple-converted-space"> </span>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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