Extracting information from gff3 file produced by augustus

Question

[Jiang]

I have finished my Eukaryotic genome annotation using augustus. I have got the gff3 file. It seems that I need to extract information from the gff3 file for the downstream functional annotation. But I don't know how to do it in linux. Could anyone provide some suggestions?

[sansan96]

For genomic feature extraction I recommend AGAT or gffread:

1. https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html

2. https://github.com/gpertea/gffread

[Istvan Albert]

you should be more specific as to what you are trying to do.

in general parsing a GFF file, while error prone and annoying it is reasonably straightforward,

look at your file with a text editor and identity what steps are you trying to achieve aka which field of which region should be extracted into what foramt