[maker-devel] gff3_merge on models only for SNAP training?

[Carson Holt]

Yes.  It's ok. Non-genic feature lines will be ignored.

--Carson

From:  Felipe Barreto <fbarreto at ucsd.edu>
Date:  Friday, May 23, 2014 at 2:31 PM
To:  MAKER group <maker-devel at yandell-lab.org>
Subject:  [maker-devel] gff3_merge on models only for SNAP training?

Hi, all,

I should have confirmed this well before starting my Maker runs, but better
now than never.

When generating a merged gff file to be used for SNAP training, is it OK to
use the default gff output from gff3_merge, which contains all protein/EST
evidence alignments (this is what I did)?  Or should I have generated a gene
models-only merged gff (using the -g flag) for training?  I assume the Maker
flag within the larger gff file will allow the subsequent scripts (e.g.
maker2zff) to ignore the other alignments, but just wanted to check.

Thanks again!

Felipe 


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