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<p class="MsoNormal">Would that include all the gene models predicted by Augustus or only the ones that Maker retains after considering all ab initio gene predictions (SNAP + Augustus) and the EST evidence?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot,</p>
<p class="MsoNormal">Elissar</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:jason.stajich@gmail.com">Jason Stajich</a><br>
<b>Sent: </b>Friday, November 25, 2022 11:51 AM<br>
<b>To: </b><a href="mailto:elissaralam@ufl.edu">Alam,Elissar</a><br>
<b>Cc: </b><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a><br>
<b>Subject: </b>Re: [maker-devel] Augustus predictions within MAKER2</p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#FA4616">[External Email]</span></b>
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<p class="MsoNormal">After you run the gff3_merge step you can <o:p></o:p></p>
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<p class="MsoNormal">grep augustus final.gff > augustus.gff3 <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Nov 23, 2022 at 8:02 AM Alam,Elissar <<a href="mailto:elissaralam@ufl.edu">elissaralam@ufl.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> </p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I ran Augustus and SNAP as part of the MAKER2 gene annotation pipeline. I would like to use the gene predictions generated by Augustus (prior to MAKER selecting the final gene model
based on all ab initio predictions) for downstream analyses. Is there a way to obtain the Augustus gene predictions in gff3 format from MAKER2?</p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks a million,</p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Elissar</p>
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<p class="MsoNormal">_______________________________________________<br>
maker-devel mailing list<br>
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<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal">Jason Stajich<br>
<a href="mailto:jason.stajich@gmail.com" target="_blank">jason.stajich@gmail.com</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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