How do I create a gff(3) file from a genebank file?

1

Hello

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 (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 (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


gff


genebank

• 34 views

This usecase is one of the many why wrote the bio package. Get the file:

bio fetch NC_022898

convert the Genbank file to GFF like so:

bio convert  NC_022898 --gff > annotations.gff

See more here:

www.bioinfo.help/bio-gff.html

note how much nicer and prettier the gene models made with bio are (plus are fully compatible with featureCounts):

Disclaimer: the package is still under heavy development and has not been sufficiently tested


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