853914db4ca301e3d1db209c24b9a951dfbb5f4a braney Sun Sep 13 17:24:41 2020 -0700 adding all the bigLolly options to doc diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index acf8896..6bd047c 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -1,122 +1,121 @@

bigLolly Track Format

-The bigLolly format is a standard bigBed file that generates a lollipop graph. -bigLolly files are compressed and indexed as bigBeds. The trackDb defines the fields used to create -the graph. +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 bigLolly files are in an indexed binary format. The main advantage of this format is that only +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.

bigLolly format definition

-Any bigBed file can be displayed as a bigLolly. +Any bigBed file can be displayed as a bigLolly. See bigBed format.

Creating a bigLolly track

-To create a bigLolly track, follow these steps to build a bigBed here

+To create a bigLolly track, follow these steps to build a bigBed here

Examples

Example #1

In this example, you will create a bigLolly custom track using an existing bigBed file, bigBed.bb, located on the UCSC Genome Browser http server. This file contains data for the hg38 assembly.

To create a custom track using this bigLolly file:

Construct a track line that references the file:

track type=bigLolly name="bigLolly Example One" description="A bigLolly file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLolly.bb linkDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLolly.link.bb

Paste the track line into the custom track management page for the human assembly hg38 (Dec. 2013).
Click the "submit" button.

Custom 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?db=hg38&position=chr22_KI270731v1_random &hgct_customText=track%20type=bigLolly%20name=Example %20bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLolly.bb %20linkDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigLolly.link.bb%20visibility=pack

After this example bigLolly is loaded in the Genome Browser, click into a chain on the browser's track display. Note that the details page displays information about the individual chains, similar to that which is available for a standard chain track.

Example #2

In this example, you will create your own bigLolly file from an existing chain input file.

Save this chain file to your computer (Step 1 in Creating a bigLolly track, above).
Save the autoSql files bigLolly.as and bigLink.as to your computer (Step 2, above).
Download the bedToBigBed and hgLoadChain utilities (Step 3, above).
Save the hg38.chrom.sizes text file to your computer. This file contains the chrom.sizes for the human hg38 assembly (Step 4, above).
Run the utilities in Steps 5-7, above, to create the bigLolly and bigLink output files.
Place the newly created bigLolly (bigLolly.bb) and and bigLink (bigLolly.link.bb) files on a web-accessible server (Step 8).
Construct a track line that points to the bigLolly file (Step 9, above).
Create the custom track on the human assembly hg38 (Dec. 2013), and view it in the Genome Browser (Step 10, above).

Sharing your data with others

If 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.

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.

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 row(s) in your input file before running the bedToBigBed program.