Format
GFF3
The successor annotation format with strict parent-child relationships and URL-encoded attributes; common from NCBI and non-model organisms.
Extensions: .gff3, .gff · Coordinates: 1-based-closed · Specification
From GFF3
- How to Convert GFF3 to GTF (and Why IDs Go Missing)
gffread -T looks like a one-command fix until your NCBI GFF3 comes out the other side missing gene_id on half its transcripts.
To GFF3
- How to Convert GTF to GFF3 (and Why IDs Go Missing)
gffread reconstructs the Parent hierarchy GFF3 demands, but only if your GTF's gene_id and transcript_id were consistent to begin with.