Browser Extensible Data (BED Files)

Introduction

BED files are tab-separated files storing genomic intervals. They come in a variety of flavors but all contain a list of chromosome, start and end values along with other data. A comprehensive overview of the format can be found at the UCSC Genome Browser FAQ page.

Tags

filetype:bedfile datatype:bedlike

Data Preparation

For BED files smaller than 10Mb, the only necessary preparation is association with an assembly. See the documentation on BAM files for instructions on how to associate a BED dataset with an assembly.

Files larger than 10Mb need to be aggregated to beddb format. See the higlass docs for documentation on how to aggregate bedfiles using clodius. Aggregated beddb files should be added to resgen with the filetype:beddb tag.