<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div>Try both ways (run in same maker directory to avoid reprocessing of evidence alignments). Then look at the output in a browser. Really the best way to decide which works best id manual evaluation.</div><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">David Carlson <<a href="mailto:david.carlson@stonybrook.edu" class="">david.carlson@stonybrook.edu</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Training Augustus using Transdecoder output</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">January 7, 2020 at 1:47:23 PM MST<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class=""></span></div><br class=""><br class=""><div dir="ltr" class="">Hi Maker users and developers,<div class="">I'm currently in the process of annotating a new genome, and I have a question regarding training Augustus.</div><div class=""><br class=""></div><div class="">I have RNA-Seq data from my organism, which I've mapped to my genome assembly with Hisat2 and assembled into transcripts with StringTie. </div><div class=""><br class=""></div><div class="">I've used these transcripts to predict proteining coding genes with Transdecoder (using homology evidence from the swissprot and Pfam databases).</div><div class=""><br class=""></div><div class="">I was thinking about taking the Transdecoder output, (after removing sequences that are not full length) and using these as the initial training set for Augustus.</div><div class=""><br class=""></div><div class="">In the past, I've used Busco for the initial Augustus training, but my thought is that these Transdecoder predicted genes might be a better source of evidence for my particular species.</div><div class=""><br class=""></div><div class="">Do any of you have experience trying this approach, or thoughts regarding its merits?</div><div class="">Thanks!</div><div class="">Dave</div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dave Carlson<br class=""></div>PhD Candidate<br class=""></div>Ecology and Evolution Department<br class=""></div>Stony Brook University</div></div></div></div></div></div></blockquote><br class=""></div></body></html>