Compare
BED vs GFF3: interval extraction and annotation structure
BED suits interval selection; GFF3 carries typed annotations, attributes and relationships.
Which format should you choose?
Consider BED for overlap or extraction and GFF3 for exchanging annotation structure.
Good fit for BED
Share target regions or browser tracks
- Interval overlap and extraction coordinates
Good fit for GFF3
Annotate genes, transcripts and exons
- Exchange feature types, attributes and relationships
Basic information
| Field | BED | GFF3 |
|---|---|---|
| Extension | .bed | .gff3, .gff |
| MIME type | ||
| Common uses | Share target regions or browser tracks | Annotate genes, transcripts and exons |
| How to open | Use a compatible tool and check assembly, chromosome names and field count. chr1 0 100 describes the first 100 bases. Block starts are relative to chromStart. | 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 | For ordinary nonempty intervals, add 1 to the start when converting to GFF3 and retain the end. Check separate rules for zero-length features. Coordinates alone cannot reconstruct annotation attributes or hierarchy. | 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
Interval overlap and extraction coordinates
Share target regions or browser tracks
BEDExchange feature types, attributes and relationships
Annotate genes, transcripts and exons
GFF3Key point 1
BED core fields are chromosome, start and end.
More on the differencesKey point 2
GFF3 uses nine tab-separated columns and attributes.
More on the differencesMore on the differences
Decide whether intervals suffice or transcript/exon relationships and CDS phase are needed. Agree on reference assembly and feature selection.
- For ordinary nonempty intervals, changing BED zero-based, end-exclusive coordinates to GFF3 one-based, inclusive coordinates adds 1 to the start. Validate zero-length and circular cases separately.
- BED extraction may discard attributes, Parent relationships and phase. Blocks do not necessarily reconstruct every GFF3 annotation; verify counts and correspondence.
Frequently asked questions
Does shifting coordinates by one support another assembly?
No. Convention conversion is not mapping between assemblies. Use appropriate mapping and record regions that could not be mapped.