BedGraph

bedGraph track is used for showing numerical values along the genomic coordinate. In the track, the genome is separated into a set of intervals and each interval is assigned to a specific numerical value.

Each line of a bedGraph track file contains four fields:

1. chromosome name
2. start, 0-based
3. stop
4. numerical value

Take following steps to prepare a bedGraph track for browser display.

1. sort the track file using "sort" command:

sort -k1,1 -k2,2n old_file > new_file

2. compress file

bgzip new_file

3. index file

tabix -p bed new_file.gz

4. move files "new_file.gz" and "new_file.gz.tbi" to a web server. The two files must be in the same directory. Obtain the URL to "new_file.gz" for submission.

Converting bigWig to bedGraph

• if you have compiled the UCSC kent source tree, you would get an utility called bigWigToBedGraph:

$ bigWigToBedGraph 
bigWigToBedGraph - Convert from bigWig to bedGraph format.
usage:
   bigWigToBedGraph in.bigWig out.bedGraph
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

• You could use this tool to convert bigWig files to bedGraph, and then tabix it as above.

• If you didn't compile the Kent source, you could also download this utility (compiled by UCSC) from UCSC website: http://hgdownload.soe.ucsc.edu/admin/exe/