Adding functional annotation and meta-data of MAKER/BRAKER GFF

Question

[javanokendo]

Happy new year, 2023. I am doing genome assembly and annotation. I have a problem doing the functional annotation part of it since I am new and still learning this. I have done the following:

1. Assembled the genome (using Verkko and Hifiasm) and assessed the assembly quality
2. Did the transcriptome assembly using trinity
3. Run MAKER and BRAKER annotation pipelines successfully and I have the gff files.
4. I did extract the proteins and transcript sequences from the maker results.

Now I am supposed to add the functional annotation and meta-data to the MAKER gff file for me to get the actual gene names. I tried to use MAKER tutorial but this seems not to work as advertised on their tutorial. I was wondering if someone can guide me in doing the last part (adding annotation and meta-data) since it is the only step which is giving me some problems. I was to get the actual gene names (symbols). I tried the AGAT (Juke34) but I am not getting the right right gene symbols. Look forward to your help.

[Juke34]

What do you mean by « I am not getting the right right gene  », could you share an example?

[javanokendo]

I want the HUGO gene symbols/names to be attached to the maker gff . In the maker gff file I have names such as augustus_masked-ptg000079l-abinit-gene-0.32-mRNA-1 but this is not informative, we need the actual gene name (symbols) in our final gff . Do you know how to update the gene manes in the gff Juke34

[Juke34]

Look at Practical about Functional annotation here: https://nbisweden.github.io/workshop-genome_annotation/schedule

And install AGAT and instead to use gff3_scripts, use agat_sp scripts

[ben@f]

Hi, did you find an effective solution for this problem? beside Agat and

[andorjkiss]

No, I have not found a solution. That workshop was not very helpful and did not provide a solution.