[maker-devel] Q on MAKER

[Carson Holt]

You need to find out where the augustus MAKER is using is installed.  Check the maker_exe.ctl file you are using, or type ‘which augustus’.

—Carson


> On Feb 5, 2016, at 3:58 PM, hcma <hcma at uci.edu> wrote:
> 
> Hi Carlson,
> 
> These are the list of directories under maker/2.31.8
> 
> bin  data  GMOD  INSTALL  lib  LICENSE  MWAS  perl  README  RELEASE  src
> 
> 
> Where can i find augustus/? Or i have to ask my system admin to install this?
> 
> Thanks.
> 
> Best Regards
> Karen
> 
> 
> 
> 
> On 2016-02-05 14:54, Carson Holt wrote:
>> Augustus gives you an entire directory rather than just a single file
>> like SNAP.  You have to take the directory and copy it to the
>> .../augustus/config/species/ directory.
>> Example:
>> …/augustus/config/species/arabidopsis/
>> Then ‘arabidopsis’ would be the species name to use with MAKER.
>> Sometimes you may have to do a second round of both SNAP and Augustus
>> training (called bootstrapping). Look at the models you get after the
>> first round, and if they look good then, the second round is probably
>> not going top be beneficial.
>> —Carson
>>> On Feb 5, 2016, at 3:42 PM, hcma <hcma at uci.edu> wrote:
>>> Hi Dr Holt,
>>> Thanks for the email. Here is my pipeline, does it seems acceptable? Any comments is welcome and much appreciated.
>>> 1. Use maker to generate training gene set:
>>> genome=all-chromosome-r1.04.fasta
>>> est=Trinity.fasta
>>> est2genome=1
>>> 2. Use output of Maker to train SNAP:
>>> maker2zff dwil-all-chromosome-r1.04.all.gff
>>> fathom genome.ann genome.dna –gene-stats
>>> fathom genome.ann genome.dna –categorize 1000
>>> fathom genome.ann genome.dna –gene-stats
>>> fathom uni.ann uni.dna –export 1000 –plus
>>> hmm-assembler.pl genome . > dwil_genome.hmm
>>> 3. Use output of Maker to train Augustus on their webserver:
>>> File used:
>>> Upload ‘export.dna’ as the genome file
>>> Upload ‘export.aa’ as the protein file
>>> 4. second and final Maker run:
>>> genome=all-chromosome-r1.04.fasta
>>> est=Trinity.fasta
>>> est2genome=0
>>> Snaphmm=output of 2
>>> How do i incorporate the output of training set of gene from Augustus web server here into this step 4?
>>> Thanks 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
>>>> [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
>