- Genome Browser
- My Data
The bigWig format is useful for dense, continuous data that will be displayed in the Genome
Browser as a graph. BigWig files are created from wiggle (wig)
type files using the program
wigToBigWig. Alternatively, bigWig files can be created
from bedGraph files, using the program
The bigWig files are in an indexed binary format. The main advantage of this format is that only those portions of the file needed to display a particular region are transferred to the Genome Browser server. Because of this, bigWig files have considerably faster display performance than regular wiggle files when working with large data sets. The bigWig file remains on your local web-accessible server (http, https or ftp), not on the UCSC server, and only the portion needed for the currently displayed chromosomal position is locally cached as a "sparse file". If you do not have access to a web-accessible server and need hosting space for your bigWig files, please see the Hosting section of the Track Hub Help documentation.
Wiggle data must be continuous and consist of equally sized elements. If your data is sparse or
contains elements of varying sizes, use the bedGraph format instead of
the wiggle format. If you have a very large bedGraph data set, you can convert it to the bigWig
format using the
bedGraphToBigWig program. For details, see Example
#3 below. Refer to
this wiki page for help in selecting the graphing track data format most
appropriate for the type of data you have.
Note that the
wigToBigWig utility uses a substantial amount of memory: approximately
50% more memory than that of the uncompressed wiggle input file. While running the
wigToBigWig utility, we recommend that you monitor the system's memory usage
top command. The
bedGraphToBigWig utility uses about 25%
more RAM than the uncompressed bedGraph input file.
To create a bigWig track from a wiggle file, follow these steps:
Step 1. Create a wig format file following the directions here. When converting a wig file to a bigWig file, you are limited to one track of data in your input file; therefore, you must create a separate wig file for each data track.
Step 2. Remove any existing "track" or "browser" lines from your wig file so that it contains only data.
wigToBigWig program from the
binary utilities directory.
fetchChromSizes script from the
same directory to create the
chrom.sizes file for the UCSC database with which you are working (e.g., hg19).
If the assembly
genNom is hosted by UCSC, chrom.sizes can be a URL like:
wigToBigWig utility to create the bigWig file from your wig file:
wigToBigWig input.wig chrom.sizes myBigWig.bw
Note that the wigToBigWig program also accepts gzipped wig input files.
Step 6. Move the newly created bigWig file (myBigWig.bw) to a web-accessible http, https, or ftp location.
Step 7. If the file name ends with a .bigWig or .bw suffix, you can paste the URL directly into the custom track management page, click "submit" and view the file as a track in the Genome Browser. By default, the file name will be used to name the track. To configure the track label or other visualization options, you must create a track line, as shown in Step 8.
Step 8. Construct a custom track using a single track line. The most basic version of the track line will look something like this:
track type=bigWig name="My Big Wig" description="A Graph of Data from My Lab" bigDataUrl=http://myorg.edu/mylab/myBigWig.bw
Paste the custom track line into the text box on the custom track management page.
autoScale <on|off> # default is on alwaysZero <on|off> # default is off gridDefault <on|off> # default is off maxHeightPixels <max:default:min> # default is 128:128:11 graphType <bar|points> # default is bar viewLimits <lower:upper> # default is range found in data viewLimitsMax <lower:upper> # suggested bounds of viewLimits, but not enforced yLineMark <real-value> # default is 0.0 yLineOnOff <on|off> # default is off windowingFunction <mean+whiskers|maximum|mean|minimum> # default is maximum, mean+whiskers is recommended smoothingWindow <off|[2-16]> # default is off transformFunc <NONE|LOG> # default is NONE
For further information on custom bigWig track settings, see the Track Database Definition Document. For more information on how bigWig settings are used in native Genome Browser tracks, see the Configuring graph-based tracks page.
In this example, you create a bigWig custom track using an existing bigWig file on the UCSC http server. The file contains data that spans chromosome 21 on the hg19 assembly.
To create a custom track using this bigWig file:
http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bwonto the custom track management page for the human assembly hg19 (Feb. 2009).
Alternatively, you can customize the track display by including track and browser lines that define certain parameters:
track type=bigWig name="Example One" description="A bigWig file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
browser position chr21:33,031,597-33,041,570
In this example, you will create your own bigWig file from an existing wiggle file.
wigToBigWigutility (step 3, above).
wigToBigWig wigVarStepExample.gz hg19.chrom.sizes myBigWig.bw
To create a bigWig track from a bedGraph file, follow these steps:
bedGraphToBigWigprogram from the binary utilities directory.
fetchChromSizesscript from the same directory to create the chrom.sizes file for the UCSC database with which you are working (e.g., hg19). If the assembly
genNomis hosted by UCSC, chrom.sizes can be a URL like
bedGraphToBigWigutility to create a bigWig file from your bedGraph file:
(Note that the bedGraphToBigWig program DOES NOT accept gzipped bedGraph input files.)
bedGraphToBigWig in.bedGraph chrom.sizes myBigWig.bw
myBigWig.bw) to a web-accessible http, https, or ftp location.
In this example, we will display a bigWig with a dynamic sequence logo using
track type=bigWig logo=on name="Example dynseq" description="A bigWig file with logo=on dynseq" visibility=full autoScale=off bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw
browser position chr21:33,037,000-33,037,050
You can also load the above by clicking this link.
If you would like to share your bigWig data track with a colleague, learn how to create a URL by looking at Example #6 on this page.
Because bigWig files are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with these files, available from the binary utilities directory.
bigWigToBedGraph— converts a bigWig file to ASCII bedGraph format.
bigWigToWig— converts a bigWig file to wig format. Note: if a bigWig file was created from a bedGraph, bigWigToWig will revert the file back to bedGraph.
bigWigSummary— extracts summary information from a bigWig file.
bigWigAverageOverBed— computes the average score of a bigWig over each bed, which may have introns.
bigWigInfo— prints out information about a bigWig file.
These utilities accept either file path names or URLs to files as input. As with all UCSC Genome Browser programs, simply type the program name (with no parameters) on the command line to view the usage statement.
In some cases,
bigWigAverageOverBed will produce very
similar results, but in other cases, the results may differ. This is due to data-handling
differences between the two programs. Summary levels are used with
therefore, some rounding errors and border conditions are encountered when extracting data over
relatively small regions. In contrast, the
bigWigAverageOverBed utility uses the actual
data, which ensures the highest level of accuracy.