<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="">Make sure you are training either SNAP or Augustus and not just protein2genome or est2genome. You can also rescue rejected Augustus/SNAP models by running them through InterProScan and then giving any model that contains an InterPro domain to the model_gff= option.<div class=""><br class=""></div><div class="">BASIC PROTOCOL 5 from this protocols paper —> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/" class="">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 3, 2021, at 1:35 PM, Adam Stuckert <<a href="mailto:stuckerta@gmail.com" class="">stuckerta@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<br clear="all" class=""><div class=""><br class=""></div><div class="">I am working on annotating several different assemblies, but I am having difficulty getting a reasonable number of predicted genes/proteins. My annotations always predict way too few genes (thousands too few) in the final transcript/protein fasta files. So, I am seeking help.</div><div class=""><br class=""></div><div class="">My approach is to annotate with EST evidence from the same species (either straight from transcriptome assemblers or predicted coding regions from TransDecoder) and use protein evidence from uniprot + related species. Simple repeats are softmasked within Maker. All repeats are masked in Maker, and I am supplying a repeat library that includes lineage-specific repeats as well as species specific repeats that are modeled by RepeatModeler2. I am using Maker version 3.01.03. <br class=""><br class="">I'm attaching my options control file. Any help to troubleshoot this would be greatly appreciated.</div><div class=""><br class=""></div><div class="">Thanks,<br class="">Adam</div><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class="">Adam Stuckert</div><div class=""><br class=""></div></div></div></div>
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