Where can I download the gff3 file for a specific human genome build? (hg38 release 77)

Question

[O.rka]

I found this: ftp://ftp.ensembl.org/pub/release-98/gff3/homo_sapiens

but there are only GTF files for release 77: ftp://ftp.ensembl.org/pub/release-77

Does anyone know where I can find this information?

[Kevin Blighe]

Oh, these are Ensembl release numbers; so, Ensembl 77 and Ensembl 98 (the title is somewhat misleading). The weekend has arrived, so, you may not receive a response from our Ensembl team members. Have you considered just converting the GTF v77 file to a gff3?

Answer 1

[Juke34]

look at here: http://www.ensembl.info/2017/07/06/gff3-and-sequence-ontology-terms/

GFF3 is provided only since release 81. SO you will have to convert it yourself. There are many tools to do so. Personally, I use gxf_to_gff3.pl from the GAAS repo.