[maker-devel] Q on MAKER

[hcma]

Hi Carson,

For the final run of annotation, I would like to incorporate tophat 
results from RNA-seq data, from your experience, do you know if it is 
better to use raw RNA-seq (Illumina paired-end data) or trimmed (trimmed 
using Trimmomatuc) data for feeding into tophat? If trimmed, do you 
recommend a particular programme?

Thanks for your time.

Best Regards
KAren




On 2016-02-05 15:33, Carson Holt wrote:
> 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
>>