BUSCO trained Augustus parameter for MAKER

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BUSCO trained Augustus parameter for MAKER

Arnab Ghosh
Hello,

I am trying to annotate genes in a non-model organism. I am using MAKER for this purpose and have trained SNAP and plan on Genemark and Augustus as well for the predictions.

After searching the google group on MAKER-devel I understand  BUSCO is a good choice for training Augustus and decided to give it a shot. From one of the earlier posts on BUSCO, I read that it is supposed to generate a species name specific folder in the config directory of Augustus. However I did not get any. The BUSCO run finished fine with the run_species folder and all necessary table, hmm folder and other files etc. generated under the run_species folder. 

Following was the command i used to run BUSCO:

python run_BUSCO.py --in mySpecies.fasta  --out my_species --long --lineage_path /usr/home/aves_odb9 --mode genome

So there was no "my_species" folder generated under the config directory of augustus.

Did I miss something ? My question is-- what should I pass to the "augustus_species" variable now in the maker control file for the next run of maker ?

Thanks so much for your time !!

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Re: BUSCO trained Augustus parameter for MAKER

Carson Holt-2
Hello Arnab,

Perhaps someone on the list will chime in with an answer for you, but you may also want to post to direct to BUSCO since your question is entirely related to BUSCO and you are more likely to get a quick response there.


Thanks,
Carson




On Jul 19, 2017, at 2:24 PM, Arnab Ghosh <[hidden email]> wrote:

Hello,

I am trying to annotate genes in a non-model organism. I am using MAKER for this purpose and have trained SNAP and plan on Genemark and Augustus as well for the predictions.

After searching the google group on MAKER-devel I understand  BUSCO is a good choice for training Augustus and decided to give it a shot. From one of the earlier posts on BUSCO, I read that it is supposed to generate a species name specific folder in the config directory of Augustus. However I did not get any. The BUSCO run finished fine with the run_species folder and all necessary table, hmm folder and other files etc. generated under the run_species folder. 

Following was the command i used to run BUSCO:

python run_BUSCO.py --in mySpecies.fasta  --out my_species --long --lineage_path /usr/home/aves_odb9 --mode genome

So there was no "my_species" folder generated under the config directory of augustus.

Did I miss something ? My question is-- what should I pass to the "augustus_species" variable now in the maker control file for the next run of maker ?

Thanks so much for your time !!
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Re: BUSCO trained Augustus parameter for MAKER

Xabier Vázquez Campos
AFAIK, the profile can be the folder run_my_species/augustus_output/retraining_parameters and the files inside would look like BUSCO_my_species_[a number]_*.*
Create a folder in the species directory and copy this in there. Note that the folder and the included files should have the same name prefix e.g. BUSCO_my_species_[a number], otherwise whenever you call the profile, Augustus is going to freak out. The prefix will be your augustus_species


On 1 August 2017 at 03:09, Carson Holt <[hidden email]> wrote:
Hello Arnab,

Perhaps someone on the list will chime in with an answer for you, but you may also want to post to direct to BUSCO since your question is entirely related to BUSCO and you are more likely to get a quick response there.


Thanks,
Carson




On Jul 19, 2017, at 2:24 PM, Arnab Ghosh <[hidden email]> wrote:

Hello,

I am trying to annotate genes in a non-model organism. I am using MAKER for this purpose and have trained SNAP and plan on Genemark and Augustus as well for the predictions.

After searching the google group on MAKER-devel I understand  BUSCO is a good choice for training Augustus and decided to give it a shot. From one of the earlier posts on BUSCO, I read that it is supposed to generate a species name specific folder in the config directory of Augustus. However I did not get any. The BUSCO run finished fine with the run_species folder and all necessary table, hmm folder and other files etc. generated under the run_species folder. 

Following was the command i used to run BUSCO:

python run_BUSCO.py --in mySpecies.fasta  --out my_species --long --lineage_path /usr/home/aves_odb9 --mode genome

So there was no "my_species" folder generated under the config directory of augustus.

Did I miss something ? My question is-- what should I pass to the "augustus_species" variable now in the maker control file for the next run of maker ?

Thanks so much for your time !!
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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