Training augustus with busco or?
Posted: Thu Mar 22, 2018 5:24 pm
Hi,
I am pretty new to augustus and the whole training process. I've somehow got gene predictions of my assembled fasta of cryptosporidium but there are genes with multiple introns and they don't make much sense. I feel like the dataset for the prediction is just wrong.
I ran busco with --fast option without any special changes to the config and got the "/augustus_output/retraining_parameters" folder which I've immediately used as new augustus species so I could run "augustus [parameters] --species=SPECIES queryfilename" where the SPECIES is a name for my newly created folder in augustus/config/species which includes the files generated by busco(/augustus_output/retraining_parameters).
I haven't run any optimization scripts at all.
Is this a bad approach, what's the best way to train augustus and then get meaningful gene predictions while all I have is MIRA output from fastq Illumina readings and the species isnt't listed in augustus manual.
Thanks much.
I am pretty new to augustus and the whole training process. I've somehow got gene predictions of my assembled fasta of cryptosporidium but there are genes with multiple introns and they don't make much sense. I feel like the dataset for the prediction is just wrong.
I ran busco with --fast option without any special changes to the config and got the "/augustus_output/retraining_parameters" folder which I've immediately used as new augustus species so I could run "augustus [parameters] --species=SPECIES queryfilename" where the SPECIES is a name for my newly created folder in augustus/config/species which includes the files generated by busco(/augustus_output/retraining_parameters).
I haven't run any optimization scripts at all.
Is this a bad approach, what's the best way to train augustus and then get meaningful gene predictions while all I have is MIRA output from fastq Illumina readings and the species isnt't listed in augustus manual.
Thanks much.