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The 5’ most junction on the 3’ terminal exon (assuming + strand) is discordant in both Annotation 1 & 2 from the evidence in Ba.
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<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>
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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.
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<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>
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<div class="">I'm probably missing something trivial. </div>
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<div class="">Thanks</div>
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<div class="">Jim<br class="">
<div class=""><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; border-spacing: 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> </div>
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