gff3 file format

Question

[bestone]

Can I use the gff3 format file as a reference genome? I added a screenshot photo of how can I find a reference genome in this picture?

Answer 1

[ATpoint]

No. Go to Assembly and download the fasta file there. That is your genome. A GTF/GFF3 file is a tabular format that contains positional information of CDS, exons etc, so gene and transcript wise information with genomic positions.

[bestone]

I am wondering why they write assembly file instead of genome file so if I used it as the reference genome to make an index from this assembly genome I won't get into any trouble right?

[GenoMax]

An assembly (file) represents the genome and will contain the sequence and just the sequence. Information about where the genes are in that sequence comes from the file you show above (GFF3).

[bestone]

Thank you for the answers, as far as I understand, if I index this assembly as a reference genome, I won't have a problem.

[GenoMax]

Correct. You have to index the sequence file (assembly in this case) for any alignments you are planning to do. These indexes are aligner specific so you may need to make them multiple times if you change aligners.

[ATpoint]

A genome is made from an assembly of sequences. It's fine, these terms are largely interchangable.