In this example, you will create a bigLolly custom track using an existing bigBed file, located on the UCSC Genome Browser http server. By default the score field is used to define the lollipop height. 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/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://genome.ucsc.edu/goldenPath/help/examples/bigBedExample3.bb %20visibility=fullhttp://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://genome.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.bbbedToBigBed -as=bigLollyExample2.as -type=bed9+1 bigLollyExample2.bed hg38.chrom.sizes bigLollyExample2.bb
track 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=fulltrack type=bigLolly name="bigLolly Example Two" description="A second bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog visibility=fullIn 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 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=on lollyMaxSize=10 yAxisNumLabels=offtrack type=bigLolly name="bigLolly Example Three" description="A third bigLolly file" bigDataUrl=http://genome.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.