Augustus command line help needed

[gomahony]

Hi

I'm trying to run Augustus in command line form to generate a FASTA file with just the predicted gene sequences and not the usual output. I can generate the usual output no problem but its the getting it to produce a FASTA file part im stuck with.

Thanks

[Fitoedu]

Hi,

yo need to include in the comand line the options:
--protein=on --codingseq=on, and finali get de gff file ( > yourannotation.gff), with the coding sequence in the output.
Next, you can obtain the coding sequences suing the script getAnnoFasta.pl included in the augustus scripts.

[rahularjun86]

Hi,
Have you tried getAnnoFasta.pl script? It is in the augustus/scripts directory.
Cheers,
Rahul