[maker-devel] Speaking of AED...

[Barry Moore]

The 5’ most junction on the 3’ terminal exon (assuming + strand) is discordant in both Annotation 1 & 2 from the evidence in Ba.

[cid:F7723E49-0CF1-4E2C-A8BF-64312129A65F]

B

On Nov 7, 2014, at 11:34 AM, Jim Hu <jimhu at email.tamu.edu<mailto:jimhu at email.tamu.edu>> wrote:

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.

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?

I'm probably missing something trivial.

Thanks

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054

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