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BEDbase public instance

The public BEDbase instance at hosts public BED files.

🚧 Documentation under construction.

Finding relevant BED files

The best way to locate data is to use the search interface on the home page. This search interface is smart. It relies on our Text2BED models, which allow you to search the genome using natural language. We have previously computed embeddings for each BED file in BEDbase, and then you can search them.

Downloading data

From the search interface, you can add results to your cart, then download all the files in your cart.


BEDsets are collections of BED files. BEDbase holds tens of thousands of files, which span reference genome assemblies. You aren't likely to want to use all the data for one project. BEDsets provide a way to group together a subset of the files in BEDbase for a particular purpose. In the future, users will be able to create their own BEDsets.