Sunday, September 9, 2012

Prepare custom track of annotation data (or "bed" track)

0 Make sure you have the tabix program installed.
You can download the latest source and compile:

Or if you're using Ubuntu operating system, install it using apt-get:
$ apt-get install tabix
You should have both tabix and bgzip programs available on your computer.

1 Skip this step if your file is BED format.

Run the command bigBedToBed in UCSC genome browser tool set and convert the bigBed file to a bed text file.

2 Compress the BED file:
$ bgzip input.bed

The old file is gone and a new file "input.bed.gz" is there instead.

3 Build tabix index of the compressed BED file:
$ tabix -p bed input.bed.gz

The "input.bed.gz" is untouched but an index file "input.bed.gz.tbi" is generated.

4 Display this file as a custom bed track on WashU Genome Browser.
Put the .gz and .gz.tbi files on the SAME directory on your web server.
Use only the URL to the .gz file to make the custom track.

The BED format used by WashU Epigenome Browser:
  1. chromosome name
  2. start coordinate
  3. stop coordinate
  4. Name (if absent, use dot)
  5. ID (unique non-negative integer)
  6. Strand (+/-/.)