bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index 633585b2d57..399899a6652 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -93,31 +93,31 @@

Go to chr21:17,030,007-17,055,589 to see the data.

Example #2

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.

Save this bed file to your computer.
Save the autoSql files bigLollyExample2.as to your computer.
Download the bedToBigBed - utility.

utility

Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human hg38 assembly.
Use the 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.bb
```

Move 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: SNP data" description="A second bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog visibility=full
```
Go to chr21:15,593,670-15,632,442 to see the data.

@@ -125,31 +125,31 @@

In this example, you will create your own bigBed file to display as a bigLolly from a bed file with the size of the lollipop defined by an extra field (lollySizeField=lollySize) where the numbers in this field are similar to a radius and define circle size. To avoid large circles from being clipped, the setting lollyMaxSize=10 ensures circles of size 10 fully display. Also, to turn off the lollipop stems, the setting lollyNoStems=on is added. Finally, the settings yAxisLabel.0="0 on 30,30,190 0" and yAxisLabel.1="5 on 30,30,190 5" adds labels and lines on the y axis where 30,30,190 defines the color.

Save this bed file to your computer.
Save the autoSql files bigLollyExample3.as to your computer.
Download the bedToBigBed - utility.

utility

Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human hg38 assembly.
Use the 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
```
Move the newly created bigBed file (bigLollyExample3.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/bigLollyExample3.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 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" lollyMaxSize=10 lollyNoStems=on
```
Go to chr21:25,891,755-25,891,870 to see the data.

@@ -165,38 +165,38 @@ This link loads the same bigLolly.bb track and sets additional display parameters from Example 1 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=full

If you would like to share your bigLolly data track with a colleague, learn how to create a URL link to your data by looking at Example #6 on the custom track help page.

Extracting data from the bigLolly format

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.

+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.

Troubleshooting

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 +(available here) to remove the problematic row(s) in your input file before running the bedToBigBed program.