Compare
BED vs bigBed: text editing and indexed delivery
BED is interval text; bigBed is indexed binary BED-type data.
Which format should you choose?
Consider BED for editable analysis input and bigBed for regional delivery of large tracks.
Good fit for BED
Share target regions or browser tracks
- Interval overlap and extraction coordinates
Good fit for bigBed
Publish large genomic annotation tracks
- Browser access to selected regions
Basic information
| Field | BED | bigBed |
|---|---|---|
| Extension | .bed | .bb, .bigBed |
| MIME type | ||
| Common uses | Share target regions or browser tracks | Publish large genomic annotation tracks |
| 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. | Open with a compatible browser or bigBed tool; verify assembly, chromosome names and field definitions. Test remote reachability and partial reads in the actual environment. |
| 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 bedToBigBed, supply one track and matching chrom.sizes. Group by chromosome and sort by start, remove track/browser lines and specify extra fields with -type/-as. |
Choose by use case
Interval overlap and extraction coordinates
Share target regions or browser tracks
BEDBrowser access to selected regions
Publish large genomic annotation tracks
bigBedKey point 1
BED rows and columns can be inspected as text.
More on the differencesKey point 2
bigBed indexes provide access to selected regions.
More on the differencesMore on the differences
Check full versus partial reads, extra-field definitions and hosting support. Do not assume it is always smaller or faster; test real data.
- Ordinary interval coordinates use BED zero-based, end-exclusive conventions in both. Creating bigBed does not map assemblies; match input and chrom.sizes references.
- Prepare one properly ordered track, remove display headers and define extra fields. Rebuild after edits and validate counts, coordinates and fields when exporting.
Frequently asked questions
Does gzip-compressed BED equal bigBed?
No. gzip alone does not create bigBed indexes. Retain source BED, field definitions and reference information.