The bigLolly format uses a standard bigBed file that is used to generate a lollipop graph. By default the score is used to decide how high to draw the lollipop, but there are trackDb options to specify which fields to use for the height and width of the lollipop, as well as to draw lines on the graph.
The bigBed files used in bigLolly type 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. The bigLolly 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 bigLolly files, please see the Hosting section of the Track Hub Help documentation.
Any bigBed file can be displayed as a bigLolly. See bigBed format.
In this example, you will create a bigLolly custom track using an existing bigBed file, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.
To create a custom track using this bigBed file:
track type=bigLolly name="bigLolly Example One" description="A bigLolly file" bigDataUrl=: http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bbtrack type=bigLolly name="bigLolly Example One" description="A bigLolly file" bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb visibility=fullCustom tracks can also be loaded via one URL line. -This link loads the same bigLolly.bb track and sets additional display parameters in the URL:
-http://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:17,002,145-17,159,243&hgct_customText=track%20type=bigLolly%20name=Example %20bigDataUrl=http://hgwdev-braney.gi.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb %20visibility=packhttp://genome.ucsc.edu/cgi-bin/hgTracks?ignoreCookie=1&db=hg38&position=chr21:17,002,145-17,159,243&hgct_customText=track%20type=bigLolly%20name=Example %20bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb %20visibility=full
In this example, you will create your own bigBed file to display as a bigLolly from an bed file. Using an extra field to define the height of the lollipops
bedToBigBed
utility .bedToBigBed utility to create a bigBed file from your sorted BED file, using
the bigLollyExample2.bed file and chrom.sizes files created above.
bedToBigBed -as=bigLollyExample2.as -type=bed9+1 bigLollyExample2.bed hg38.chrom.sizes bigLollyExample2.bbMove the newly created bigBed file (bigLollyExample2.bb) to a web-accessible http, https, or ftp location. At this point you should have a URL to your data, such as "https://institution.edu/bigLollyExample2.bb", and the file should be accessible outside of your institution/hosting providers network. For more information on where to host your data, please see the Hosting section of the Track Hub Help documentation.
-track type=bigLolly name="bigLolly Example Two" description="A second bigLolly file" bigDataUrl=http://hgwdev-braney.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLogtrack type=bigLolly name="bigLolly Example Two" description="A second bigLolly file" bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog visibility=full-In this example, you will create your own bigBed file to display as a bigLolly from an bed file with the size of the lollipop defined by an extra field, and the height defined by the score field.
+In this example, you will create your own bigBed file to display as a bigLolly from an bed file with the size of the lollipop defined by an extra field, and the height defined by the score field. We'll also turn off the lollipop stems and add some labels and lines on the y axis.bedToBigBed
utility .bedToBigBed utility to create a bigBed file from your sorted BED file, using
the bigLollyExample3.bed file and chrom.sizes files created above.
bedToBigBed -as=bigLollyExample3.as -type=bed9+1 bigLollyExample3.bed hg38.chrom.sizes bigLollyExample3.bb
track type=bigLolly name="bigLolly Example Two" description="A third bigLolly file" bigDataUrl=http://hgwdev-braney.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb lollySizeField=lollySize visibility=full position=chr21:25,891,748-25,891,877track type=bigLolly name="bigLolly Example Three" description="A third bigLolly file" bigDataUrl=http://hgwdev.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb lollySizeField=lollySize visibility=full yAxisLabel.0="0 on 30,30,190 0" yAxisLabel.1="5 on 30,30,190 5" lollyNoStems=onIf you would like to share your bigLolly data track with a colleague, learn how to create a URL by looking at Example 6 on this page.
Because the bigLolly files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the binary utilities directory.
bigBedToBed — converts a bigBed file to ASCII BED format.bigBedSummary — extracts summary information from a bigBed file.bigBedInfo — prints out information about a bigBed file.As with all UCSC Genome Browser programs, simply type the program name (with no parameters) at the command line to view the usage statement.
If you encounter an error when you run the bedToBigBed program, check your input
file for data coordinates that extend past the the end of the chromosome. If these are present, run
the bedClip program
(available here) to remove the problematic
row(s) in your input file before running the bedToBigBed program.