[maker-devel] Quick question about re-annotation

[Carson Holt]

Yes the advice given so far is correct.  You can pass back through old
evidence using the maker_gff option and setting est_pass, protein_pass, etc.
to 1.  Set the pred_pass=0 so as to ignore old predictions.  Let MAKER
generate those again to reflect the additional evidence (added to the
alt_est= option).  If you have model_pass=1 and map_forward=1 set then if
any model changes, you can at least maintain the name.

Thanks,
Carson


From:  Jason Stajich <jason.stajich at gmail.com>
Date:  Sunday, 17 June, 2012 12:30 AM
To:  Daniel Standage <daniel.standage at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Quick question about re-annotation

Well remember that ESTs are used as extra helper information to the ab
initio gene predictors so it will want to run all those predictions again
and re-call the gene structures from the combined output with this extra
info added in. So you will need to decide how you want these to be
incorporated and if you are willing to wait for the analysis to complete
again with this info. The pass through of the previous run will allow you to
keep the names from that previous run if they are important to you.

Jason Stajich


On Thu, Jun 14, 2012 at 7:48 PM, Gowthaman Ramasamy
<gowthaman.ramasamy at seattlebiomed.org> wrote:
> Of course, Carson knows the best answer.
> 
> But, I think, you need to grab the GFFs from your previous maker run, and pass
> it as model_gff= option. That way, gene models in GFFs are used as a starting
> point and now will check for evidences from your alt_est dataset....
> 
> -Gowthaman
> ________________________________________
> From: maker-devel-bounces at yandell-lab.org
> [maker-devel-bounces at yandell-lab.org] On Behalf Of Daniel Standage
> [daniel.standage at gmail.com]
> Sent: Thursday, June 14, 2012 11:26 AM
> To: Maker Mailing List
> Subject: [maker-devel] Quick question about re-annotation
> 
> Greetings!
> 
> I have a quick question about re-annotation with Maker. I have successfully
> completed a Maker run, but now I would like to re-run Maker with some
> additional EST evidence (from a related organism, aligned and in GFF3 format).
> I simply added the file to the altest_gff configuration setting and re-ran
> Maker. However, from  the log messages it looked like Maker was starting from
> scratch rather than using what had already been completed in the initial run.
> Luckily, I had made a backup of the complete Maker data structure, so I killed
> the job, deleted the data structure, and restored from the backup.
> 
> Before I try to run this again, do I need to change any other configuration
> settings to do this re-annotation? The stanza under Re-annotation Using MAKER
> Derived GFF3 looks relevant, but it is not clear to me which settings need to
> be set.
> 
> Thanks!
> 
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
> 
> 
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