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extrinstic.cfg
Posted: Fri Nov 20, 2015 1:24 pm
by katharina
Originally posted in the old forum by Anna on 29.10.2012 - 11:16
Could you, please, explain how could I adjust the parameters in extrinstic.cfg file?
Best, Anna
Re: extrinstic.cfg
Posted: Fri Nov 20, 2015 1:24 pm
by katharina
by katharina on 29.10.2012 - 12:34
The format of the extrinsic.cfg file is explained for example at
http://bioinf.uni-greifswald.de/bioinf/ ... Aseq.GSNAP in section 6.1
We do not provide an automated protocol for adjusting those parameters to the specific needs of a particular genome/hints combination.
Usually, we execute AUGUSTUS with the default parameters, first, then we inspect the predicted genes in the context of extrinsic evidence in a genome browser, and then we adjust the parameters according to those results.