Additional resources
Hubs can be loaded into the URL using the hubUrl= parameter. This parameter
takes input similar to the track hub input box.
Native UCSC supported genomes can be loaded into the URL using the db= parameter while
non-natively supported genomes such as assembly hubs or GenArk hubs use the genome=
parameter. URL parameters can be combined by using &.
The following example links to the hg19 genome database and an example track hub using the db= and the hubUrl= parameters:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubDirectory/hub.txt
Track hubs' track visibility can also be changed from the URL parameters. As an example, the following link specifies:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1+
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1>exRnaSignalMaleYoung_hideKids=1>exRnaSignalMaleYoung=full>exRnaSignalSRR1311243=full&ignoreCookie=1
guidelines=on/off - activate or deactivate the blue guidelineshgFind.matches=<listOfNames> - highlight features given their nameshgt.reset=1 - show only the default trackshgt.toggleRevCmplDisp=1 - show the reverse-complementhgt.labelWidth=<number> - set the size of the left-side label areahideTracks=1 - hide all trackshideTracks=1&<trackName>=full|dense|pack|hide - hide all tracks and show
other trackshighlight=<db>.<chrom>:<chromStart>-<chromEnd>#<color>|...After defining the "groups.txt" file, tracks can be assigned to a specific group within the "trackDb.txt" file using the group setting. For example, to assign the "bigBed1" track to the "category1" group, you could use the following stanza:
track bigBed1
-bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
+bigDataUrl https://hgdownload.gi.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
shortLabel bigBed example 1
longLabel This bigBed file is an example from the NCBI RefSeq Diffs Track
type bigBed
group category1
visibility denseThe full "trackDb.txt" file, which includes the "bigBed1" track and additional examples, can be viewed here: trackDb.txt.
Next, incorporate the "groups.txt" file with the groups setting into the genome stanza. This can be for a UCSC genome, a GenArk assembly, or an assembly hub. Below is an example using the hg38 genome:
@@ -953,31 +953,31 @@
Browser software attempts to speed performance by reading the trackDb architecture into
a separate cache. This software assumes that the timestamp on a file like a hub's trackDb.txt should
always be increasing in time and never decreasing (i.e., a new update to the file should not have
an earlier timestamp). We did discover that if someone were to copy an older file (say with
cp -p to preserve file timestamp), for example to restore a trackDb.txt to an earlier
version, they might get stuck with a hub that is not updating. To resolve this specific problem the
person would only need to edit or touch the file and give it a new timestamp.
Hubs can be checked for valid file configuration, trackDb keywords, and composite or super track settings with the Hub Development tool. This tool can be accessed from the Track Hub page under the Hub Development tab. After entering your URL in the search box, -the tool runs the hubCheck utility program equivalent to:
hubCheck -noTracks http://url.to.hub.txt
The noTracks setting speeds up the validation process but does not check for the presence or validity of your remotely hosted data track files. This tool checks your hub.txt, genome.txt, and trackDb.txt settings and displays warnings and errors in bright red font, such as "Missing required setting..." and "Cannot open...". The "Display load times" and "Enable hub refresh" optional settings show the load timing at the bottom of the Genome Browser page and allow instant hub refresh instead of 5 minute refresh. These options can be checked and activated by clicking "View Hub on Genome Browser". The following picture shows the example track grouping hub with the warning that the hub has no hub description page, no configuration errors, and "Display load times" checked:
@@ -1003,31 +1003,31 @@ hubCheck http://yourHost/yourDir/hub.txt options: -checkSettings - check trackDb settings to spec -version=[v?|url] - version to validate settings against (defaults to version in hub.txt, or current standard) -extra=[file|url] - accept settings in this file (or url) -level=base|required - reject settings below this support level -settings - just list settings with support level Will create this directory if not existing -noTracks - don't check remote files for tracks, just trackDb (faster) -udcDir=/dir/to/cache - place to put cache for remote bigBeds and bigWigsNote that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.
The hubCheck program is available from the UCSC downloads server at -http://hgdownload.soe.ucsc.edu/admin/exe/.
+http://hgdownload.gi.ucsc.edu/admin/exe/.If the browser is unable to load a track hub, it will display an error message. Some common causes for an import to fail include typos in the URL, a hub server that is offline, or errors in the track hub configuration files. Occasionally, remote track hubs may be missing, off-line, or otherwise unavailable. If a user is already browsing data from the remote hub when it disconnects, a yellow error message will be displayed instead of the expected data.
You can use the command-line utility hubClone to download all of the @@ -1041,50 +1041,50 @@
Here is the usage message for the hubClone utility:
hubClone - Clone the remote hub text files to a local copy in newDirectoryName, fixing up bigDataUrls to remote location if necessary
usage:
hubClone http://url/to/hub.txt
options:
-udcDir=/dir/to/udcCache Path to udc directory
-download Download data files in addition to the hub configuration files
Note that you will have to use the -udcDir option if /tmp/udcCache is not writable on your machine.
The hubClone program is available from the UCSC downloads server at -http://hgdownload.soe.ucsc.edu/admin/exe/.
+http://hgdownload.gi.ucsc.edu/admin/exe/.The Genome Browser supports searching for items within bigBed tracks in track data hubs. To support this behavior you have to add an index to the bigBed file when you initially create the the bigBed file from the bed file input. Indices are usually created on the name field of the bed, but can be created on any field of the bed. Free-text searches can also be enabled by creating a TRIX index file that maps id's in the track to free-text metadata. Further instructions can be found in the Searchable Hub Quick Start Guide.
See the searchIndex and searchTrix fields in the Hub Track
Database Definition document for
information on how to set up your bigBed to enable searching. The searchIndex setting requires
the input BED data to be case-senstive sorted (sort -k1,1 -k2,2n). You can use
either the example UNIX sort command or the bedSort utility available
-here. See an example
+here. See an example
searchable hub.
The Genome Browser supports three varieties of data filter options for bigBed data. These can improve data usability in many ways, such as displaying specific data by default (e.g. only items that pass certain quality scores), allow for filtering based on pre-specified categories (e.g designate only LINE repetitive elements from a list of options) and more.
For more information on the options available and examples on how to set up filters, see our Track Hub Filters Quick Start Guide and the filter entries in the