[maker-devel] Q on MAKER

[Carson Holt]

I recommend using both.  You probably don't have augustus installed.

--Carson

Sent from my iPhone

> On Feb 5, 2016, at 4:20 PM, hcma <hcma at uci.edu> wrote:
> 
> 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
>