[maker-devel] Q on MAKER

[Carson Holt]

You need to view the output the programs produce, not the HMM. You can Run them through MAKER and then view the GFF3 files produced

Here is a MAKER tutorial where this is done that you can follow along if you wish —> http://gmod.org/wiki/MAKER_Tutorial_2013#Training_ab_initio_Gene_Predictors <http://gmod.org/wiki/MAKER_Tutorial_2013#Training_ab_initio_Gene_Predictors>

For Augustus training there are a number of threads related to how to do that on the MAKER mailing list archives — https://groups.google.com/forum/#!searchin/maker-devel/augustus <https://groups.google.com/forum/#!searchin/maker-devel/augustus>
Also other resources online —> http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html <http://www.molecularevolution.org/molevolfiles/exercises/augustus/training.html>

—Carson




> On Feb 11, 2016, at 5:18 PM, hcma <hcma at uci.edu> wrote:
> 
> Hi Carson,
> 
> I have downloaded Apollo and what format of the SNAP and Augustus models does Apollo take? Do i need to reformat the SNAP.hmm and which output of Augustus to use if I train Augustus manually?
> 
> Thanks again for your time.
> 
> Best Regards
> Karen
> 
> 
> 
> 
> On 2016-02-05 06:36, Carson Holt wrote:
>> Hi Karen,
>> There are many ways to train Augustus. I prefer to identify gene
>> models in MAKER (GFF3) and use those to train both SNAP and Augustus.
>> Here is a previous post on the topic —>
>> https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ <https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ>
>> [1]
>> In the end you need to look at the SNAP and Augustus models together
>> with evidence alignments in a genome browser (like desktop Apollo).
>> When everything is trained well, both SNAP and Augustus models will
>> look like each other and both seem to look like the evidence
>> alignments.
>> Thanks,
>> Carson
>>> On Feb 4, 2016, at 5:52 PM, hcma <hcma at uci.edu> wrote:
>>> Hi,
>>> I have a genome sequence and Trinity assembly for a new species and
>>> I am wondering what are the best steps to take when using MAKER?
>>> 1. I used the genome sequence and all assembled Trinity sequence to
>>> do first run of MAKER in order to generate training set for SNAP and
>>> Augustus.
>>> In maker_opts.ctl:
>>> genome=all-chromosome-r1.04.fasta
>>> est=Trinity.fasta
>>> est2genome=1
>>> 2. Train SNAP
>>> 3. Train Augustus
>>> When i train Augustus, i only supply genome and protein file, should
>>> i also supply the trinity file here?
>>> 4. what's the best parameter to use when running MAKER the second
>>> time for obtaining the final annotation? I would prefer not to use
>>> any external protein data.
>>> genome=all-chromosome-r1.04.fasta
>>> est=Trinity.fasta
>>> est2genome=0
>>> SNAP
>>> Augustus
>>> Thanks.
>>> Best Regards
>>> KAren
>> Links:
>> ------
>> [1]
>> https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ <https://groups.google.com/forum/#!searchin/maker-devel/augustus/maker-devel/FWMSTdqWQqI/lC3miQtiCpwJ>
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