Compare
GTF vs GFF3: attribute syntax and transcript mapping
Both use nine annotation columns, but attribute syntax and relationship models differ.
Which format should you choose?
Use compatible GTF when analysis requires it; consider supported GFF3 for hierarchical annotation exchange.
Good fit for GTF
Share gene, transcript and exon positions
- Annotation input for expression tools requiring GTF
Good fit for GFF3
Annotate genes, transcripts and exons
- Exchange feature types, attributes and relationships
Basic information
| Field | GTF | GFF3 |
|---|---|---|
| Extension | .gtf | .gff3, .gff |
| MIME type | ||
| Common uses | Share gene, transcript and exon positions | Annotate genes, transcripts and exons |
| How to open | Use a GTF-aware tool to inspect assembly, sequence names, delimiters and attributes. Match exons and CDS by transcript ID; check required feature types and column-eight values against reader rules. | Use a GFF3-aware tool to check version directive, reference names, nine columns and attribute escaping. Validate ID/Parent references; repeated IDs may describe one discontinuous feature rather than accidental duplicates. |
| Export or convert | Map gene_id/transcript_id to appropriate GFF3 ID/Parent relationships. Renaming attributes alone is insufficient. Validate row correspondence, coordinates, strand, CDS and retained attributes; keep originals. | For ordinary interval extraction to BED, subtract 1 from the start and retain the end. Decide how features are selected or merged; retain originals when attributes, hierarchy or CDS phase are lost. |
Choose by use case
Annotation input for expression tools requiring GTF
Share gene, transcript and exon positions
GTFExchange feature types, attributes and relationships
Annotate genes, transcripts and exons
GFF3Key point 1
GTF uses attributes such as gene_id "value";.
More on the differencesKey point 2
GFF3 uses attributes such as ID=value;Parent=value.
More on the differencesMore on the differences
Agree on feature types, transcript IDs, attributes and reader interpretation, not just extension or column count.
- Ordinary coordinates are one-based and inclusive in both; no BED-style start adjustment is needed. Validate assembly, strand, CDS column eight and stop-codon treatment against producer conventions.
- Explicitly map GTF identifiers and GFF3 hierarchy, multiple parents and discontinuous features. Record unsupported features or attributes; check count changes and retain originals.
Frequently asked questions
Can attribute renaming alone convert between them?
No. Syntax, relationship models and producer rules differ. Compare features per transcript and retained attributes after conversion.