<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="">Final gene models will have ‘maker' in the source column. All others are not gene models, but rather evidence alignments that are there for reference. Make sure you specified a gene predictor during the maker run, or you may only have alignments and no models. Anything with protein_gff:protein2genome in the source column would fall into the category of evidence alignment.<div class=""><br class=""></div><div class="">I do not believe GAG supports tRNA’s. Someone may be able to correct me, but I believe they only support the coding annotations.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 23, 2018, at 7:43 AM, Giroux, Emily (CFIA/ACIA) <<a href="mailto:Emily.Giroux@inspection.gc.ca" class="">Emily.Giroux@inspection.gc.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">After running my rounds with Maker, I went on to using the Genome Annotation Generator (GAG) and tbl2asn to find errors and fix them. My plan is to run BLAST and InterProScan after so that I don’t waste time annotating invalid features. However, when running GAG, all the protein_gff:protein2genome annotations get removed, along with the Name matches that I got to related species. Somehow I feel it would be better to find the errors, and go back to the last Maker generated gff3 instead of continuing on successively with each GAG-cleaned-up gff. However, another thing is that the start and stop codons are not included in the Maker gff, and there is no way that I can fix this all in the original manually.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">My question is, is it a real loss to lose the protein_gff:protein2genome information, and all the Name info, or does this get added back once I run BLAST and InterProScan? Does Maker have a function to add the Start and Stop codons? Should I really be running BLAST and InterProScan before going on to GAG? Lastly, MAKER adds tRNA annotations, but for each of these, tbl2asn results in errors: SEQ_FEAT.MissingTrnaAA, and I’m not sure if I can just ignore this…<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Emily</div></div></div></blockquote></div><br class=""></div></body></html>