If you have tracks across multiple assemblies, see the full track hub documentation.
The most common track types are bigBed and bigWig. Compressed, binary versions of -the corresponding plain-text formats. Together they should cover most +the corresponding plain-text formats. Together, they should cover most of what you might want to display in the Genome Browser, from transcription peaks to RNA-seq signals.
You can use bigBed tracks to display discrete annotations, such as genes, transcription start sites, or conserved genomic elements. The bigBed format builds off the plain-text BED format and is thus flexible in terms of what fields are included. Your file must start with a minimum of 3, and up to 12, standard fields, but can also extend the format with any number of additional fields.
bedToBigBed utility for your system type from
our download
server.
bedToBigBed to build your bigBed:
bedToBigBed -sort in.bed chrom.sizes myBigBed.bbbigDataUrl setting in your hub.txt.
Once you have built your bigBed files, it is time to create a stanza in your hub.txt file for that track. Here is what the required settings discussed above might look like for a basic bigBed track:
track bigBedRequiredSettings
shortLabel bigBed Required Settings
longLabel A bigBed Example with Required Settings
visibility pack
type bigBed 12 +
bigDataUrl gtexCaviar.chr7_155799529-155812871.bb
The type line consists of three parts: +
The type line consists of three parts:
Here is a screenshot of what this basic bigBed track looks like displayed in the Genome Browser:
-The bigBed format also offer a wide range of customization options for the -display, from decorators to highlights. Additionally, it offer extensive +The bigBed format also offers a wide range of customization options for the +display, from decorators to highlights. Additionally, it offers extensive filter controls, searching options, and mouseover configurations. Our trackDb documentation contains a full listing of settings available for the format.
Here is the bigBed configuration with some commonly used settings, including filtering and mouseover configuration.
track bigBedCommonSettings
shortLabel bigBed Common Settings
longLabel A bigBed Example with Commonly Used Settings
visibility pack
type bigBed 12 +
@@ -215,64 +208,64 @@
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
If you're working with a
GenArk assembly hub (e.g. GCF/GCA), then the chrom.sizes
file can be found under the "Data file downloads" section on the
assembly gateway page.
Put your bigWig file alongside your hub.txt in a web-accessible location,
either through the 10GB of space we
make available to users or through one of several
other services.
You will use the file name (e.g. "myBigWig.bw") with the bigDataUrl setting.
bigWig track hub configuration
-The basic trackDb configuration for a bigWig track is similar to a bigBed track as
+The basic trackDb configuration for a bigWig track is similar to a bigBed track, as
all tracks require the same basic settings (track, shortLabel, longLabel, type, bigDataUrl).
This is what the configuration for a bigWig track might look like (the example
hub.txt includes other useful settings):
track bigWigExample
shortLabel bigWig Example
longLabel A bigWig Example with Commonly Used Settings
visibility pack
type bigWig -20 10.003
bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw
color 60,60,140
-The type line consists of two parts:
+
The type line consists of two parts:
- "bigWig" is the basic track type
- "-20 10.003" indicates the minimum and maximum of the data in the bigWig
Here is what this looks like visualized in the Genome Browser:
Grouping tracks
Next, we'll provide a basic overview of how to group your tracks using
composite tracks and super tracks. This will allow you to pull similar data
together under a single container.
Composite Tracks
Composite tracks can hold multiple tracks of the same type. For example, you
-use a composite to group together a set of RNA-seq experiments including
+use a composite to group together a set of RNA-seq experiments, including
replicates.
Here's what the configuration might look like for a composite containing two
bigWig tracks. There are two key components of a composite: (1) the line
"compositeTrack on" in the parent track stanza, and (2) including "parent
compositeName" for each track that will be part of the composite.
track compositeExample
shortLabel Example Composite Track
longLabel Example composite track using bigWigs
visibility dense
type bigWig
compositeTrack on
track compositeBigWig1
@@ -338,45 +331,47 @@
bigDataUrl a.chr7_155799529-155812871.bw
shortLabel ST bigWig composite #1
longLabel A composite-contained bigWig in a super track example #1
parent superTrackCompositeBigWig on
type bigWig 0 1
track superTrackCompositeBigWig2
bigDataUrl c.chr7_155799529-155812871.bw
shortLabel ST bigWig composite #2
longLabel A composite-contained bigWig in a super track example #2
parent superTrackCompositeBigWig on
type bigWig 0 1
-Loading the example hub with this super track onfiguration looks like this:
+Loading the example hub with this super track configuration looks like this:
Creating description pages
If you plan to share your track hub more widely, you will want to create a description page for your tracks.
A description page could contain a short description of what the data represents, how the data was generated,
-a link to the associated paper, or a contact email for questions regarding the data.
+a link to the associated paper, or a contact email for questions regarding the data. Multiple tracks can use
+the same description page.
+
We provide an example description html that you can modify with
the details for your track. Once you've modified this example html for your
-track add an html to the corresponding track stanza:
+track, add an html to the corresponding track stanza:
track bigWigExample
shortLabel bigWig Example
longLabel A bigWig Example with Commonly Used Settings
type bigWig -20 10.003
bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw
html bigWigDescription.html
Sharing your hub
Once you have a functional hub that you would like to share with others, you
can create links that you give to others in two ways.
@@ -385,28 +380,28 @@
Load your hub, configure the genome browser as you'd like (e.g. position and
data tracks), select "My Sessions" under "My Data", and use the option to save
the current settings as a session. You will then be provided with a URL that
you can share with others.
The other option is to create a URL to the Genome Browser that loads your hub
on the assembly of interest. There are three URL parameters
you will want to use:
db - UCSC assembly name (e.g. hg38)
position - chromosome position to load
hubUrl - URL to your hub
-You will then append these to a genome browser URL. For example, this url with load the example hub:
+You will then append these to a genome browser URL. For example, this url loads the example hub:
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr7:155799529-155812871&hubUrl=https://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubBasicSettings/hub.txt
If you feel that your hub would be of general use to the research community,
you can contact us about making it a public hub. Note that public hubs have to meet
more stringent requirements than the basics described here.
Check that your hub meets the public hub requirements
and then follow the directions on that page for submitting it to us for review.