Bactopia-tools eggnog - decorate_gff option

[steven-bioinfo]

Dear bactopia team,

I use bactopia and then bactopia-tools eggnog for my genomic prokaryote analyse.
As output i want to have a gff file with prokka and eggnog annotation merged in the same gff file.

It's possible with the option --decorate_gff of eggnog-mapper, but to have the annotation merged from the same file we need to give the gff prokka file as input for each sample.

It is possible to do this with the --eggnog_opts ?
It's working with the --decorate_gff yes option but I don't see how I can do it with a gff filename because they're different for each sample

Thanks,

Steven

[rpetit3]

Hmmm, I think this should be possible.

I looks like I would just need to have the gff brought in with the proteins fasta file. Let me think about how to implement this, but again, I think it should be straightforward.

Do you think it would be useful to make it the default behavior (e.g. --decorate_gff FILE)?

[steven-bioinfo]

Hello,

Yes for me it is the most interesting to concatenate the annotation information from the different software and not predict again genes.

I my case, I use the faa and the gff from prokka as input to doesn't predict the genes a second time but just add the eggnog annotations.