bed

.bed — BEDGraph

University of California, Santa Cruz · 2009

Developer
University of California, Santa Cruz
Category
GIS & Maps
MIME Type
text/bedgraph
First Released
2009
Open Format
Yes
File Signature
N/A (plain text, no specific header signature)
At a Glance
.bed
BEDGraph

BEDGraph is a text-based format for storing and visualizing genomic data tracks along chromosomes.

Reviewed on August 2, 2026
Compression
Plain text
Transparency
No
Editability
High
Best for
Genomic data tracks

Key Features

  • Plain text, human-readable format.
  • Stores continuous data values over genomic regions.
  • Supports integration with genome visualization tools.
  • Simple, tab-delimited structure for easy parsing.

Best For

  • Storing quantitative genomic data.
  • Creating genome browser tracks for visualization.
  • Exchanging genomic data with analysis pipelines.
  • Simple, uncompressed data representation.

Less Ideal For

  • Storing raw sequencing reads (use FASTQ or BAM).
  • Representing discrete genomic features like genes (use BED format).
  • Large-scale data storage requiring compression.
  • Complex genomic annotations beyond a single value.

Common Use Cases

  • Visualizing ChIP-seq or RNA-seq data coverage.
  • Displaying methylation levels across the genome.
  • Representing gene expression data or epigenetic modifications.
  • Mapping copy number variations (CNVs).

How to Open It

  1. Open with a text editor (like Notepad, VS Code, Sublime Text) to view the raw data.
  2. Load into genome browsers like the UCSC Genome Browser or IGV (Integrative Genomics Viewer).
  3. Import into bioinformatics analysis software that supports the BEDGraph format.
  4. Process programmatically using scripting languages like Python or R.

What is a .bed file?

BEDGraph is a plain text file format used primarily in bioinformatics to store genomic data. It represents data tracks over genomic coordinates, making it excellent for visualizing variations in data along a genome. Each line in a BEDGraph file typically contains a chromosome, a start position, an end position, and a value associated with that genomic region. This straightforward structure allows for easy parsing and compatibility with various genome visualization tools.

Programs That Open .bed Files

PlatformProgram
WindowsIntegrative Genomics Viewer (IGV)Free
VS CodeFree
macOSIntegrative Genomics Viewer (IGV)Free
VS CodeFree
LinuxIntegrative Genomics Viewer (IGV)Free
VS CodeFree
Web BrowserUCSC Genome BrowserFree

How to Convert .bed Files

FormatMethod
.BIGWIGbedGraphToBigWig utility
.WIGbedGraphToWig utility

Common Problems with .bed Files

⚠️ Incorrect chromosome naming or coordinate systems.
Ensure consistency in chromosome naming (e.g., 'chr1' vs '1') and use 0-based start/1-based end coordinates as expected by the tool.
⚠️ Value errors or non-numeric data.
Verify that the fourth column contains valid numerical data suitable for the intended visualization or analysis.
⚠️ Large file sizes slowing down loading.
Consider converting to a binary format like BigWig for better performance with large datasets.

Frequently Asked Questions

What is the main difference between BED and BEDGraph formats?▼

The standard BED format is used for discrete genomic features (like genes or exons), while BEDGraph is used for quantitative data values that vary across genomic regions (like read coverage or expression levels).

Can BEDGraph files be compressed?▼

BEDGraph is a plain text format and is not inherently compressed. For larger datasets, it's common to convert BEDGraph files to compressed binary formats like BigWig for faster loading and smaller file sizes.

What software can I use to view BEDGraph files?▼

Genome browsers like the UCSC Genome Browser and the Integrative Genomics Viewer (IGV) are excellent for visualizing BEDGraph data. You can also open them with any text editor to inspect the raw data.

Technical Details

BEDGraph files are plain text, with each line formatted as chrom, chromStart, chromEnd, value. The data is not compressed and is directly human-readable. Its simplicity makes it efficient for genome browsers to parse and display as continuous or discontinuous tracks.

Did You Know?

BEDGraph was developed at the University of California, Santa Cruz (UCSC), a major hub for bioinformatics research.
Its simplicity allows it to be easily generated by many sequencing data analysis pipelines.

Security Information

BEDGraph files are plain text and do not typically contain executable code, making them generally safe to open. However, always ensure you are downloading files from trusted sources, as with any data file.