Error when trying to convert exonerate output to gff3

Question

[Mike]

edit: seems to be working OK when I use EVM's Exonerate_to_gff3.pl script.

Hi all, I used exonerate protein2genome mode and got a gff file:

Now when I try to convert it to gff3 using gffread I get this:

Error parsing attribute gene_id ('"' required for GTF) at line:

Chr01 exonerate:protein2genome:local gene 12952001 12955830 3036 + . gene_id 1 ; tr|I1J698|I1J698_SOYBN; gene_orientation + ; identity 100.00 ; similarity 100.00 e

Any ideas what can I do to fix it? My goal is to convert the files i got from different gene prediction methods and use them as input for EVM (EVidenceModeler).

Thank you!

[mrmrwinter]

Before you get a better answer, I would look into using AGAT for cases like this. Seems like its the kind of thing it would be able to do.

https://github.com/NBISweden/AGAT

[Junior]

Hey can anyone share the parameter for exonerate to generate gff file? My settings gave me a C4 alignment output files that contain target/querry sequences and alignment. My goal is to extract querry/target sequences. All packages that extract sequences from gff using genome.fasta files are enable to do so with the kind of output I am getting

Answer 1

[Juke34]

AGAT can probably deal with that indeed.

Otherwise the problem is that the format is not respected: For GTF: Attributes’ values should be surrounded by double quotes which is not the case here. On top of that, to be proper GTF you need a semicolon at the end of each feature line. See here for more information https://agat.readthedocs.io/en/latest/gxf.html

[Mike]

Hey Juke! Thanks for the suggestion, AGAT seems great.

I hope you don't mind me asking but, why is there such a big difference in size between the AGAT versions?

[Juke34]

No problem. Could you elaborate? What did you see? The github repo or the tool/lib installation?

Prior v0.8.0 I was using R by default to make some plots. So it was installing R and plenty of related dependencies. Since >=v0.8.0 I removed R by default. It is still possible to make plots in scripts handling it but you need install R and the dependecies yourself. That made a serious change in size.

If you look at the size of the repo, the v.0.9.0 contain ppt from PAG2022 presentation, which is 6Mb size so that make a serious size change.