[maker-devel] Q on MAKER

[Michael Campbell]

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
>