<div dir="ltr">Steven - <div><br></div><div>You might start with the galaxy install and tutorial or the cyverse one.<div><a href="https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html">https://galaxyproject.github.io/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html</a></div><div><a href="https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html">https://learning.cyverse.org/projects/sciapps_guide/en/latest/annotation.html</a></div><div><a href="http://gmod.org/wiki/MAKER_Tutorial">http://gmod.org/wiki/MAKER_Tutorial</a><br></div><div>Not sure if the space needed will be too much for your large genome. To gain better help you might specify the problems you are having in running or installing?</div><div><br></div><div>I'll also point out a parallel genome annotation tool we have built called funannotate which does the prediction training automatically from BUSCO or RNASeq datasets. </div><div><a href="https://funannotate.readthedocs.io/en/latest/">https://funannotate.readthedocs.io/en/latest/</a> - </div><div><br></div><div>installation with conda <a href="https://funannotate.readthedocs.io/en/latest/install.html">https://funannotate.readthedocs.io/en/latest/install.html</a> </div><div> also docker image.</div><div><a href="https://hub.docker.com/r/nextgenusfs/funannotate">https://hub.docker.com/r/nextgenusfs/funannotate</a><br></div><div><a href="https://github.com/reslp/funannotate-docker">https://github.com/reslp/funannotate-docker</a><br></div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><br></div><div dir="ltr">Jason Stajich<br></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 5, 2021 at 6:17 PM Steven L. Miller <<a href="mailto:Fungi@uwyo.edu">Fungi@uwyo.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p style="margin:0px 0px 2px 6px;font-stretch:normal;line-height:normal">
<font face="ComicSansMS" style="font-family:ComicSansMS">Sorry to say probably not a new issue. </font><font face="ComicSansMS" style="font-family:ComicSansMS">I saw that MAKER is an easy-to-use genome annotation pipeline </font><span style="color:rgb(34,34,34);background-color:rgb(255,255,255)">designed
to be usable by small research groups with little bioinformatics experience. That statement describes me to a t.
</span><span style="font-family:ComicSansMS"> </span><font face="ComicSansMS" style="font-family:ComicSansMS">I am new to Whole Genome Sequencing and associated analysis, and have a limited skill set with computers. </font><font face="ComicSansMS" style="font-family:ComicSansMS">I
have a </font><span style="font-family:ComicSansMS">a 1.52 GB, 75k unitigs, non-photosynthetic vascular plant assembly for which I would like to predict functional genes. </span>I have tried to follow the tutorial that you have posted for Winter
School 2018 to see if I can duplicate your installation and implementation for my HPC. <font face="ComicSansMS" style="font-family:ComicSansMS">I doubt that you will be impressed, but I recently received a “certificate” for completing our HPC Linux
course path the University of Wyoming. </font><font face="ComicSansMS">. I realize now how much I don’t know and how much work it will take to complete an annotation, but I am needing to generate at least some preliminary data to include in an upcoming
grant submittal (~2 months). </font></p>
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<div> I read your MAKER wiki page, but it seems that it hasn’t been completed in many cases, with many important parts (important parts to me, in any case) under construction.</div>
<div style="font-family:ComicSansMS"><br>
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<div style="font-family:ComicSansMS">I am writing to get any help I can to find a way forward in my project. Any suggestions and any help you can provide would be gratefully accepted!</div>
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<p style="font-family:ComicSansMS;margin:0px 0px 2px 6px;font-stretch:normal;line-height:normal">
<span>Sincerely,</span><br>
<span>Steve Miller</span><br>
<span>Botany</span><br>
<span>University of Wyoming</span></p>
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