UTR Training Question - copying the contents the utr.pbl file of another species
Posted: Thu Nov 19, 2015 2:45 pm
Originally posted by Allison F in the old forum on 08.01.2015 - 21:09
I was able to train my gene model using the autoAug.pl script to generate the following files in my species gene model directory:
My_fish_exon_probs.pbl
My_fish_metapars.cfg
My_fish_weightmatrix.txt
My_fish_exon_probs.pbl.withoutCRF
My_fish_metapars.cgp.cfg
My_fish_igenic_probs.pbl
My_fish_metapars.utr.cfg
My_fish_igenic_probs.pbl.withoutCRF
My_fish_parameters.cfg
My_fish_intron_probs.pbl
My_fish_parameters.cfg.orig1
My_fish_intron_probs.pbl.withoutCRF
My_fish_parameters.cfg.orig2
The autoAug.pl program was unable to complete the UTR training, therefore I am manually training the UTR’s. I am following the “Training AUGUSTUS UTR parameters” tutorial instructions (found here : http://bioinf.uni-greifswald.de/bioin ... TRTraining) and it states that “If the file /pathToYourAUGUSTUS/config/species/yourSpecies/yourSpecies_metapars.utr.pbl does not exist, yet, you need to create it, e.g. by copying the contents the utr.pbl file of another species.”
I am generating a gene model for a fish species. I went through the species models provided by Augustus. Some of the gene models (i.e. zebrafish) do not seem to have a utr.pbl file. I copied the human_utr_probs.pbl from the human gene model to my fish gene model directory. Was that the correct thing to do?
Confirmation that I am interpreting the tutorial instructions correctly would be greatly appreciated!
Thank you,
Allison
I was able to train my gene model using the autoAug.pl script to generate the following files in my species gene model directory:
My_fish_exon_probs.pbl
My_fish_metapars.cfg
My_fish_weightmatrix.txt
My_fish_exon_probs.pbl.withoutCRF
My_fish_metapars.cgp.cfg
My_fish_igenic_probs.pbl
My_fish_metapars.utr.cfg
My_fish_igenic_probs.pbl.withoutCRF
My_fish_parameters.cfg
My_fish_intron_probs.pbl
My_fish_parameters.cfg.orig1
My_fish_intron_probs.pbl.withoutCRF
My_fish_parameters.cfg.orig2
The autoAug.pl program was unable to complete the UTR training, therefore I am manually training the UTR’s. I am following the “Training AUGUSTUS UTR parameters” tutorial instructions (found here : http://bioinf.uni-greifswald.de/bioin ... TRTraining) and it states that “If the file /pathToYourAUGUSTUS/config/species/yourSpecies/yourSpecies_metapars.utr.pbl does not exist, yet, you need to create it, e.g. by copying the contents the utr.pbl file of another species.”
I am generating a gene model for a fish species. I went through the species models provided by Augustus. Some of the gene models (i.e. zebrafish) do not seem to have a utr.pbl file. I copied the human_utr_probs.pbl from the human gene model to my fish gene model directory. Was that the correct thing to do?
Confirmation that I am interpreting the tutorial instructions correctly would be greatly appreciated!
Thank you,
Allison