[maker-devel] Failing to recoup all gff annotations, including ab-initio

[Freeman, Robert M.]

Thanks, Carson. This explains the behavior I saw and will help us moving forward.

Best,
Bob

On Mar 19, 2013, at 10:52 AM, Carson Holt wrote:

Ab initio models without evidence support are not considered final models by default (newly trained ab initio predictors tend to have a very high false positive rate).

If you really want the ab initio models without support to upgraded, set the keep_preds=1 in the maker_opts.ctl file.  All ab inito models are also stored in the GFF3 as match/mtach_part features for reference purposes not gene/mRNA/exon/CDS.

Thanks,
Carson


From: "Freeman, Robert M." <Bob_Freeman at hms.harvard.edu<mailto:Bob_Freeman at hms.harvard.edu>>
Date: Tuesday, 19 March, 2013 9:03 AM
To: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: [maker-devel] Failing to recoup all gff annotations, including ab-initio

Carson et al.,

Thanks again for a great suite tools!

We're using MAKER now to generate gene models (and model fragments) for a ciliate, the models for which we'll be using to generate a high-quality protein database for searches with mass spec.

I bootstrapped the process using the core set of proteins with CEGMA, then trained SNAP. After the final round of running MAKER, I get about 1100 evidence-based models and 34K ab-initio. And that's fine (for now).

I am able to collect the fasta files for both transcripts and proteins (evidence-based and ab-initio) without problem.

My problem is that when I use the gff3_merge script, I only get annotations for the evidence-based models. I'm not sure why the ab-initio model annotations are being collected. I've tried using and not the '-g' switch, but this doesn't seem to make a difference.

Thoughts?

Tx,
B


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-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace





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