[maker-devel] Q on MAKER

[hcma]

Hi Mike,

Thanks for the reply. So i can input raw RNA-seq reads to Tophat and 
feed the output to maker?

Thanks.

Best Regards
KAren



On 2016-02-10 06:17, Michael Campbell wrote:
> HI Karen,
> 
> From my experience trimming reads will not make things worse and it
> generally makes things better. As far as the best program to use, one
> doesn’t really stand out above the others as far as I can tell.
> However, with paired end reads it is important to use a trimmer that
> preserves the pairing between the two files (i.e when an entire read
> is discarded the paired read is moved into a file for singletons).
> 
> Thanks
> Mike
> 
>> On Feb 9, 2016, at 5:35 PM, hcma <hcma at uci.edu> wrote:
>> 
>> 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
>>