The standard display mode for a bigBed track is a simple block or exon/intron marker in the window. Extra fields in the bigBed, however, can contain a variety of additional data. When data in the extra fields meet the schema described below, then the simple block display can be replaced with a positional heatmap. The heatmap provides a sparse 2-dimensional grid for information like expression of allele-specific point mutations across a transcript.
A heatmap bigBed file starts with the standard 12 BED fields, but adds 7 more. In a heatmap,
the standard BED blockCount, blockSizes, and chromStarts
fields define the columns of the grid (one column per block), while the extra field
@@ -221,31 +221,31 @@
chr1 1000 2000 T1 1000 + 1000 2000 0 4 1,100,100,1 0,100,700,999 2 "Case 1","Case 2" -5,0,5 #0000ff,#ffffff,#ff0000 ,2.8,,,,-4,8.9,, ,"2.8, medium","no data",,,"-4, low","8.9, extreme",,, "Example on transcript 1"
chr1 1200 2400 T2 1000 - 1200 2400 0 4 1,100,100,1 0,200,900,1199 2 "Case 1","Case 2" -5,0,5 #0000ff,#ffffff,#ff0000 ,0.1,-2,,,1.1,-3.5,, ,"0.1, negligible","-2, low",,,"1.1 marginal","-3.5 low",, "Example on transcript 2"
Here is this example in a BED file (using tabs as field separators), and the corresponding bigBed file. The bigBed was created from the BED file using the following command:
bedToBigBed -tab -type=bed12+ -as=heatmap.as heatmap.bed chrom.sizes heatmap.bb
A copy of heatmap.as is available here. chrom.sizes files for most assemblies can be found on our download server.
Once you have created a bigBed file, you need to tell the Genome Browser to display it
as a heatmap rather than a standard bigBed track. This is done by adding the
style heatmap setting to your
track's trackDb configuration. Without this setting, the browser will render the file as an
ordinary bigBed track and the heatmap extra fields will be ignored.
The most common way to load a heatmap track is through a track hub. A minimal trackDb entry for a heatmap track looks like this:
track myHeatmap