Parsing augustus output

Question

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I have performed gene model prediction using AUGUSTUS and I want to parse the output in the from of fasta file and gff/gtf file can any one suggest?

Answer 1

[opplatek]

I know it's quite late but in case somebody else has the same question. Augustus has a bunch of scripts for the postprocessing in the installation directory under augustus-x.x.x/scripts/. The basic parsing script is called getAnnoFasta.pl and takes the resulting gtf/gff as the input and outputs two files, one with nucleotide fasta (.codingseq) and the other one with protein fasta (.aa). I guess you can find other useful scripts there as well.