AUGUSTUS Forum

Originally posted in the old forum by wentao wan on 29.08.2015 - 02:57
Dear sir,
when I use the whole genome web service , I can get seven results. For example,augustus.aa , augustus.codingseq , augustus.gff ... But when I run Augustus locally, I only get one result. Although the one result obtain the seven results above, I want to know, how can I get aa sequence and codingseq ,respectively, by setting parameter.
Thank you!

by Katharina on 31.08.2015 - 08:57
The AUGUSTUS release contains a script getAnnoFasta.pl which will extract the requested files from the AUGUSTUS output. The number and type of files depends on the parameters AUGUSTUS was run with.

Would you tell me how the .gtf file is made? I see a gtf2gff.pl script but not the other way.

ddrddr wrote:Would you tell me how the .gtf file is made? I see a gtf2gff.pl script but not the other way.

I don't know if this is the only way it is done, but it looks like the .gtf file is simply the .gff lines that match /\tAUGUSTUS\t/. At least, that is how autoAugPred.pl does it.

You are correct, simply grep lines that match \tAUGUSTUS\t.

Exception: if you ran AUGUSTUS with --gff3=on, then you will get a gff3 file, not a gtf file.