<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">I think I would agree. Annotation 1 is a perfect match to the evidence. It is ab initio 1 that would have been AED of 0.2, but annotation 1 should have been AED of 0.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 7, 2014, at 11:34 AM, Jim Hu <<a href="mailto:jimhu@email.tamu.edu" class="">jimhu@email.tamu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">I was teaching Yandell and Ence (2012) in the genomics class I co-teach, and was having trouble understanding the values for AED in Box 4 Figure Bb derive from the evidence set in Figure Ba. <div class=""><br class=""></div><div class="">Box 4 says: "AAED is caculated in the same manner as SN and SPm but in place of a reference gene model, the coordinates of the union of the aligned evidence (see panel Ba) are used instead". In the union, I expect that a bp that is in an exon in any of the evidence would be considered a TP. If so, then why isn't nt-level AED for Annotation 1 in Bb zero?</div><div class=""> </div><div class="">I'm probably missing something trivial. </div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class="">Jim<br class=""><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">=====================================<br class="">Jim Hu<br class="">Professor<br class="">Dept. of Biochemistry and Biophysics<br class="">2128 TAMU<br class="">Texas A&M Univ.<br class="">College Station, TX 77843-2128<br class="">979-862-4054</span>
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