
**I can't which of the following files were used to create the GFF3 files?** 

ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.toplevel.fa.gz
ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

or an entirely different one from the ftp:
ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/

The gff3 file I am using is the following:
ftp://ftp.ensembl.org/pub/grch37/current/gff3/homo_sapiens/Homo_sapiens.GRCh37.87.gff3.gz
Hi O.rka,

The GFF3 file contains all annotated features on all sequences, including chromsomes, regions not assembled into chromosomes and
haplotype/patch regions.

Therefore, the corresponding FASTA files will be one of the toplevel files here: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/

Toplevel sequences unmasked:
   Homo_sapiens.GRCh37.dna.toplevel.fa.gz

 Toplevel soft/hard masked sequences:
   Homo_sapiens.GRCh37.dna_sm.toplevel.fa.gz
   Homo_sapiens.GRCh37.dna_rm.toplevel.fa.gz

There are further details and descriptions of the file names in the README:
ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/README

Best wishes

Ben
Ensembl Helpdesk