[maker-devel] Augustus training within Maker

[Daniel Hughes]

heya,

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
>
>
AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the
earlier tier_types, the results of these stages e.g. protein alignments
etc., are then 'synthesised' into 'hints' (early tier_type 3) that are
provided to ab initio predicters capable of taking external 'hints' - such
as augustus - that are used to generate the final models (after further
adjustmnets wrt., utrs etc.). that is to say i think what you mean by first
and second maker runs are actually internal usage of ab initios that occur
at different stages of any single maker run and you should be shielded from
this.

dan.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20121115/be1deff4/attachment-0003.html>