Annotation with eggNOG-mapper

Question

[pablo]

Hello everyone,

I have assembled a bacterial genome from PacBio reads. I would like know annotate that genome.

I used egg-mapper to do that. Prodigal detects 4131 CDS and egg-mapper outputs an GFF annotation file. Is there a way to filter that GFF, in order to know the % of functionnally annotated CDS and the % of un-annotated CDS ?

Also, I converted that GFF into a GenBank format with seqret , but the positions are wrong. In the *.genepred.fasta file from Prodigal, the positions are well indicated but not in the GFF from eggmapper, nor in the *annotations file. Do you know how to get those information?

Best