c5f99c872ca8a06458c33f93547e8b551556f48f brianlee Wed Jan 29 12:49:55 2020 -0800 Adding a doWiggle entry for custom track lines -and fixing a " needed in the page, refs #24857 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 74041b0..7ca861a 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -591,31 +591,31 @@ ≤ 166 167-277 278-388 389-499 500-611 612-722 723-833 834-944 ≥ 945
  • group=<group> - Defines the annotation track group in which the custom track will display in the Genome Browser window. By default, group is set to "user", which causes custom tracks to display at the top of the track listing in the - group "Custom Tracks". The value for "group" must be the + group "Custom Tracks". The value for "group" must be the "name" of one of the predefined track groups. To get a list of allowable group names for an assembly, go to the table browser and select "group: All Tables" "table: grp" and "get output" where entries in the "name" column may be used and some examples include "genes","regulation" and "rna".
    (Note that mirrors may define other group names in the grp table and that the group setting does not work in track hubs, but does apply for assembly hubs.)
  • priority=<priority> - When the group attribute is set, defines the display position of the track relative to other tracks within the same group in the Genome Browser window. If group is not set, the priority attribute defines the track's order relative to other custom tracks displayed in the default group, "user".
  • db=<UCSC_assembly_name> - When set, indicates the specific genome assembly for which the annotation data is intended; the custom track manager will display an error if a user attempts to load the track onto a different assembly. Any valid UCSC assembly ID may be @@ -635,30 +635,40 @@ this track. This URL will be used in the details page for the track. Any "$$"in this string this will be substituted with the item name. There is no default for this attribute.
  • htmlUrl=<external_url> - Defines a URL for an HTML description page to be displayed with this track. There is no default for this attribute. A template for a standard format HTML track description is here.
  • bigDataUrl=<external_url> - Defines a URL to the data file for BAM, CRAM, bigBed, bigWig or VCF tracks. This is a required attribute for those track types. There is no default for this attribute.
    • +
  • + doWiggle=<on> - The doWiggle setting enables BAM custom tracks + to be displayed as bar graphs where the height is proportional to the number of reads mapped + to each genomic position. This display is described as a density graph and is best viewed with + the track set to full and scaling set to auto-scale. See the Track Database Definition + doWiggle entry + for more information about the use in hubs and the + configuring BAM tracks and the + configuring graph-based tracks + help pages to learn how to further change the display.

    • Here is an example of a properly formatted track line using the bigBed format, with accompanying browser line:

    browser position chr21:33,031,597-33,041,570
 track type=bigBed name="bigBed Example One" description="A bigBed file" bigDataUrl=http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb

    Sharing your annotation track with others

    To make your Genome Browser annotation track viewable by people on other machines or at other sites, follow the steps below.

    Step 1. Put your formatted annotation file on your web site. Be sure that the file permissions allow it to be read by others.