1. Generate bigBed file
  2. Submit custom bigBed track
  3. bigBed generator

Generate bigBed file

Refer to the Kent W J bioinformatics 2010 paper for general description about bigBed as well as bigWig file formats. For file format specification, refer to bbiFile.h in Kent Source Tree.

bigBed file can be generated from BED file. Prepare your genomic feature data into a BED file with following requirements:

  1. Only 6 fields allowed (chr name, start, stop, name, id, strand)
  2. 5th field is unique integer as unique identifiers for each genomic feature

In original BED format specification, 5th field is score. Here it is replaced to ID to work with the Browser's panning mechanism.

Conversion from BED file to bigBed file is done using "bedToBigBed" program in UCSC Kent Source Tree. You can find compiled binaries here.

Submit custom bigBed track

STEP 1 - set up a web server, most commonly with Apache. Besure to enable byte-range request.

STEP 2 - place bigBed file at a directory on your web server, and obtain the file URL (domain name and relative path to the file).

STEP 3 - follow instructions below to submit custom bigBed track.

At control panel, go to "Tracks" → "Custom track", click tab "bigBed" to show the custom bigBed track submission panel:

Replace the sample bigBed file URL with your file URL, and assign a track name. Then you can click button to submit that track. Following is screenshot of the sample custom bigBed track with name "aa bb":

Each genomic feature or item in the bigBed file is plotted as a filled box. Item name is printed inside box if it fits in, or else is printed on box's left side. Item strand is indicated by ">" or "<" inside box. Unlike gene model tracks, bigBed tracks cannot incorporate structural information.

Once submitted, the custom bigBed tracks will be registered in a table at upper position in control panel:

It will also appears in track selection box, where it can be chosen for various purposes:

bigBed generator

For your convenience, you can use this function to easily generate a bigBed file by providing a list of genes. Refer to bigBed generator chapter for details.


Last modifed: 1/1/2012