Format Atlas

Guides

Handing off genomic annotations and signal tracks

Separate annotations from numerical signals and agree on the reference genome, coordinates, units and viewer. This is distinct from preserving raw reads or alignments.

Which format should you choose?

Choose by the role each file plays in your workflow.

  • Agree on meaning and reference
  • Validate display copies
  • Test the recipient's environment

Agree on meaning and reference

Record the assembly version, chromosome names and coordinate convention. Do not confuse BED-style zero-based, half-open intervals with other conventions. Document signal units, normalization and the distinction between missing values and zero.

Validate display copies

Convert BED annotations to bigBed or bedGraph signals to bigWig as appropriate. Check sorting, chromosome lengths and extra-column definitions. Compare representative output intervals and values with the source, including bigWig single-precision rounding and display summaries.

Test the recipient's environment

Supply files, conversion settings, checksums and display settings. Open the same reference and intervals in the recipient's viewer. For a Track Hub, also validate configuration files and hosting.

Formats to consider

bigBed

Good for: Serving indexed annotation tracks

Less suitable for: Treating continuous numerical signals as annotation items

bigWig

Good for: Serving interval-based numerical signals

Less suitable for: Preserving gene–transcript hierarchies unchanged

Before you export

  • An unlisted hub may still be accessible to anyone who knows its URL. Hiding a URL is not access control; use an approved environment for sensitive data.
  • Keep source data. Matching displays or checksums does not prove analytical correctness, and display summaries are not identical to original interval values.

Related comparisons

BED vs bigBed: text editing and indexed deliveryBED is interval text; bigBed is indexed binary BED-type data.bedGraph vs bigWig: numeric text and indexed deliverybedGraph is interval-value text; bigWig is an indexed numeric track.BED vs GFF3: interval extraction and annotation structureBED suits interval selection; GFF3 carries typed annotations, attributes and relationships.GTF vs GFF3: attribute syntax and transcript mappingBoth use nine annotation columns, but attribute syntax and relationship models differ.

Guides

Choosing Sequencing Files by WorkflowRaw reads, alignment inspection, analysis storage and sharing need different information. Manage references, indexes and preservation settings alongside formats.

References and specifications