[maker-devel] Quick question about re-annotation

[Gowthaman Ramasamy]

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