[maker-devel] Augustus training within Maker

[es9]

Thank you to you both for clarifying this ... I was get a smidge 
confused and reading previous posts I can see the answer had already 
been asked and replied to. Next time I will cruise the archives before 
posting!

Regards,
Eleanor


> Dan is correct about the workings of the hint based communication
> between MAKER and the gene predictors - and just to clarify further.
> MAKER never 're-trains' Augustus or any of the other gene predictors.
> Many people will retrain the gene predictors between iterative MAKER
> runs, but this is a manual (and for Augustus non-trivial) step.
>
> B
>
> On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote:
>
>> Aha - that makes sense, so with every run Augustus is run with the
>> BLAST hints available, thanks for clarifying this
>>
>> Ele
>>
>> On 15 Nov 2012, at 11:14, Daniel Hughes wrote:
>>
>>> 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.
>>
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>
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
>
>
>
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-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.