[maker-devel] Q on MAKER

[hcma]

Hi Carlson,

Thanks for the instruction and in maker_exe.ctl, i only see path to 
snap, but not to augustus, so my system admin is checking this for me.

 From some manual i found, people use both snap and augustus when using 
MAKER to annotate genomes. Would you recommend using both or one of the 
2 is sufficient?

Thanks for your valuable time and advise.

Best Regards
Karen





On 2016-02-05 15:03, Carson Holt wrote:
> 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
>>