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  • Augustus command line help needed

    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

  • #2
    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.

    Comment


    • #3
      Hi,
      Have you tried getAnnoFasta.pl script? It is in the augustus/scripts directory.
      Cheers,
      Rahul
      Rahul Sharma,
      Ph.D
      Frankfurt am Main, Germany

      Comment

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