a6a236e1f1855cb202d1824435bdf797cf07ad47 braney Mon Nov 2 16:24:47 2020 -0800 add support for bigLolly custom tracks and specifying lolly trackDb fields that specify a field using the name of the field OR the field number diff --git src/hg/htdocs/goldenPath/help/bigLolly.html src/hg/htdocs/goldenPath/help/bigLolly.html index 6bd047c..6e6dbc7 100755 --- src/hg/htdocs/goldenPath/help/bigLolly.html +++ src/hg/htdocs/goldenPath/help/bigLolly.html @@ -14,89 +14,107 @@ 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. See bigBed format.

Creating a bigLolly track

-

-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 +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 bigLolly file: +To create a custom track using this bigBed file:

  1. 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
    2. + 
    track type=bigLolly name="bigLolly Example One" description="A bigLolly file" bigDataUrl=: http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb
  2. Paste the track line into the custom track management page for the human assembly hg38 (Dec. 2013).
  3. 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
+
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=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.

+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

  1. - Save this chain file to your - computer (Step 1 in Creating a bigLolly track, above).
    2. + Save this bed file to your + computer .
  2. - Save the autoSql files bigLolly.as and - bigLink.as to your computer (Step 2, - above).
    3. + Save the autoSql files bigLollyExample2.as and
  3. - Download the bedToBigBed and hgLoadChain - utilities (Step 3, above).
    4. + Download the bedToBigBed + utility .
  4. Save the hg38.chrom.sizes text file to your computer. This - file contains the chrom.sizes for the human hg38 assembly (Step 4, above).
    5. + file contains the chrom.sizes for the human hg38 assembly . +
  5. +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" description="A second bigLolly file" bigDataUrl=http://hgwdev-braney.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample2.bb lollyField=pValueLog
    6. +
+
  • +

    Example #3

    +

    +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.

    +
    1. - Run the utilities in Steps 5-7, above, to create the bigLolly and bigLink output - files.
      2. + Save this bed file to your + computer .
    2. - Place the newly created bigLolly (bigLolly.bb) and and bigLink - (bigLolly.link.bb) files on a web-accessible server (Step 8).
      3. + Save the autoSql files bigLollyExample3.as + to your computer
    3. - Construct a track line that points to the bigLolly file (Step 9, above).
      4. + Download the bedToBigBed + utility . +
    4. + Save the hg38.chrom.sizes text file to your computer. This + file contains the chrom.sizes for the human hg38 assembly .
      5. +
    5. +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
      +

      +

    6. +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" description="A third bigLolly file" bigDataUrl=http://hgwdev-braney.gi.ucsc.edu/goldenPath/help/examples/bigLollyExample3.bb lollySizeField=lollySize visibility=full position=chr21:25,891,748-25,891,877
      7. +
  • 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.