[maker-devel] doubt about selection of the best model

[Xabier Vázquez Campos]

Hi Maker developers and users,

After quite a bit of time dealing with Maker, I can run it without problems
(thank you Carson). However, I have doubts about the evaluation of the best
model produced by Maker.

I found the AED_cdf_generator.pl script while searching in the mail list
and it is great but, when you use it, what gff files are you comparing? I
initially thought that the models to be compared where those from each *ab
initio* program, e.g. SNAP vs Augustus, and inside them, the subsequent
bootstrap training steps, but unless you run only one each time you run
Maker, the XXX.all.gff file will contain data from both predictions. Should
I run them individually?

Following the topic, Maker will generate different FASTA files for proteins
and transcripts from each program (Maker and each *ab initio* predictor) as
well as "non_overlapping" files. Which one(s) do you select to continue
with the functional annotation?

Thank you in advance,

Xabier

-- 
Xabier Vázquez Campos
*PhD Candidate*
Water Research Centre
School of Civil and Environmental Engineering
The University of New South Wales
Sydney NSW 2052 AUSTRALIA
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