Background I'm trying to analyse a RNA-seq experiment of Bacillus subtilis PY79. As part of that, I need to create an ensemble database using ensembldb (https://bioconductor.org/packages/release/bioc/html/ensembldb.html). For this I need a gff file of the genome. I tried to download it from NCBI, however, I get an error because that gff file lacks "gene_id". Since I cannot find any other gff file of that subspecies, I am now trying to generate it from the gb file.
The Problem I have a genebank (gb) file which I have downloaded from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NC_022898.1?report=genbank then send to -> file -> GeneBank (full)). I wish to convert it to a gff3 file. I have attempted several things, but no succeeded.
What I've Tried
- I tried the julia package BioJulia/GenomicAnnotations.jl, but run into an error (https://github.com/BioJulia/GenomicAnnotations.jl/issues/7). I have searched earlier cases of the same query (https://www.biostars.org/p/134589/).
- I have managed to download bp_genbank2gff3.pl, but found no instructions that helped me to run it properly.
- I have tried to find gff tools. I go to https://bmi.inf.ethz.ch/supplements/gff-tools, but only find a link to a place where I can run it online, but I'm not actually able to add any input to the online interface.