[maker-devel] Passing extra options to augustus in maker?

[Carson Holt]

You can't pass externally generated augustus hint files into maker.  But
if you do decide to run augustus alone using the hint file you just
generated, you can then pass the results in to pred_gff (after any
necessary formatting fixes for correct GFF3).

The results of running exonerate2hints.pl are essentially the same as
letting MAKER generate its own hints file because maker is using exonerate
to generate the alignment.  So the effect of an external hint file would
be essentially redundant.  When running augustus in MAKER, it is ran a
minimum of 2 times.  The first time it is run without hints and only using
the training parameters from the augustus species files.  The second time
MAKER internally generates hints based on exonerate alignments and then
runs augustus using those hints.  If you also pass in your external run,
you would then have 3 augustus runs on the genome with MAKER selecting the
model from the pool of runs that best matches the evidence alignments.

Thanks,
Carson




On 12-07-27 10:30 AM, "Fourie Joubert" <fourie.joubert at up.ac.za> wrote:

>Hi
>
>Could anyone advise me regarding passing additional options to augustus
>when running maker?
>
>I have generated a series of hints files
>(http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=Augustus.Incorpo
>rateProteins) 
>that work fine when running augustus stand-alone, but would like to be
>able to pass the necessary parameters to augustus when running maker so
>that augustus uses the hints files.
>
>Alternatively, if I need to run augustus stand-alone with the hints
>files, which option should I use to load the resulting augustus gff
>files into maker (protein_gff, other_gff, ...)?
>
>Thanks and regards!
>
>Fourie
>
>-- 
>--------------
>Prof Fourie Joubert
>Bioinformatics and Computational Biology Unit
>Department of Biochemistry
>University of Pretoria
>fourie.joubert at up.ac.za
>http://www.bi.up.ac.za
>Tel. +27-12-420-5825
>Fax. +27-12-420-5800
>
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