<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="">Do they have no AED or an AED value of 0. A value of 0 means a perfect match to the evidence.<div class=""><br class=""></div><div class="">Also make sure you are not looking for AED in the predictions (i.e. GFF3 source column snap/augustus that are of type match/match_part). Those are rejected models and will not have quality statistics calculated for them (they are only there as alignments for reference purposes).</div><div class=""><br class=""></div><div class="">Only models with the source column of ‘maker’ and a type of 'gene/mRNA/exon/CDS’ represent the gene models and will have AED and QI values.</div><div class=""><br class=""></div><div class="">You can force MAKER to also calculate quality statistics for rejected models by altering pred_stats in the maker_opts.ctl file. </div><div class=""><br class=""></div><div class="">pred_stats=0 #report AED and QI statistics for all predictions as well as models</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 13, 2018, at 9:53 PM, <a href="mailto:wangzhennan@ioz.ac.cn" class="">wangzhennan@ioz.ac.cn</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><p class="">Hi, </p><p class=""> When I used maker to get the AED value, some transcripts have no AED values in the result. Why? I used the RNA-Seq data and protein to run maker.Thank you.</p><p class=""> Best wishes.</p><p class=""><br class=""></p><p class=""> Wang</p><p class="">T</p>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@box290.bluehost.com" class="">maker-devel@box290.bluehost.com</a><br class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></div></body></html>