quwstion about outfile

Discussions about WebAUGUSTUS, the Web Service of AUGUSTUS.

Moderator: bioinf

Post Reply
User avatar
katharina
Site Admin
Posts: 530
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

quwstion about outfile

Post by katharina »

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!
User avatar
katharina
Site Admin
Posts: 530
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

Re: quwstion about outfile

Post by katharina »

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.
ddrddr
Posts: 3
Joined: Thu Feb 04, 2016 8:17 pm

Re: quwstion about outfile

Post by ddrddr »

Would you tell me how the .gtf file is made? I see a gtf2gff.pl script but not the other way.
ddrddr
Posts: 3
Joined: Thu Feb 04, 2016 8:17 pm

Re: quwstion about outfile

Post by ddrddr »

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.
User avatar
katharina
Site Admin
Posts: 530
Joined: Wed Nov 18, 2015 6:14 pm
Location: Greifswald
Contact:

Re: quwstion about outfile

Post by katharina »

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.
Post Reply