How to convert a genebank file to a gff file

Question

[Aura]

I have a .gb file from a bacterial genome and I would like to convert in an annotated .gff file. Can such a thing be done in Galaxy? Also, Is there any .gff version that fits better for working with SNP .bam files and mapping .bam files in Galaxy?

Answer 1

[thackl]

I don't know how to do it with Galaxy directly. But you can du this with seqret of the EMBOSS package

seqret -feature -osformat2 gff3 -outseq FILE.gff FILE.gb

Also BioPerl offers format conversion scripts.

[thackl]

Okay should work on Galaxy as well: http://galaxy.berkeleybop.org/tool_runner?tool_id=genbank2gff

[Aura]

Thanks! I will check the Galaxy option now, but I'll check the others too, to get more options later.