[maker-devel] Speaking of AED...

[Mark Yandell]

And you are still missing one-- 3-prine end of the middle exon is also discordant. . I agree though somehow the color makes it hard to see. Sorry. 

--mark


Mark Yandell
Professor of Human Genetics
H.A. & Edna Benning Presidential Endowed Chair
Co-director USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:801-587-7707

________________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Barry Moore [bmoore at genetics.utah.edu]
Sent: Saturday, November 08, 2014 5:07 PM
To: Jim Hu; maker-devel at yandell-lab.org
Cc: Barry Moore
Subject: Re: [maker-devel] Speaking of AED...

Hmm, I missed the one Daniel pointed out, and then upon inspection noticed a third discordant exon.  This figure needs to go into a book of optical illusions!

[cid:87ED4E8E-56C4-4808-A7E3-9F0B4521CADB]

On Nov 8, 2014, at 4:38 PM, Barry Moore <bmoore at genetics.utah.edu<mailto:bmoore at genetics.utah.edu>> wrote:

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

<PastedGraphic-1.png>

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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