How to convert .gff3 to .gff

Question

[nakanomasayuki265]

Please tell me how to convert .gff3 to .gff. I would like to use Gff2GeneTable function in clusterProfiler.

Answer 1

[Philipp Bayer]

Normally a gff3 file and a gff file should be indistinguishable to most parsers (in fact often a gff file is a gff3 file, but not always), do you get an error in Gff2GeneTable when you load your gff file?

Have a look at what a gff3 validator tool such as this one tells you about your gff file, if it doesn't complain then it's a valid gff3 file.

[emily.giroux.science]

I'm having the same issue as well. I have a gff3 output from Blast2GO, and it fails with the online validator tool that you mentioned. I was also wondering how to convert it to a gff, instead of a gff3, so that I can use the GFF2GeneTable function mentioned by nakanomasayuki.