[maker-devel] Augustus training within Maker

[Eleanor Stanley]

Hi,

Could you please confirm something for me:

If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone.
I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run.

To achieve this, do I need to change anything in maker_opts.ctl or do I leave
augustus_species= #Augustus gene prediction species model

as is, or should it be edited for the 2nd run?

Many thanks
Eleanor

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