UCSC's track hubs allow multiple wig files to be displayed in a single custom track. Thus possibly overlaying multiple types of data or displaying strand specific read depth. Individual sub-tracks within a custom track can then be toggled on/off.
The official documentation of UCSC's track hubs can be found at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.
Essentially you need a server that can be accessed via http, https, or ftp. Setting up the track hub, besides the custom track files, requires several configuration files. Below is how I placed all of the files:
./hub.txt
./genomes.txt
./myDirectory/trackDb.txt
./myDirectory/brain1.bw
./myDirectory/brain2.bw
The above assumes you have two BigWig files named brain1.bw and brain2.bw which are in a directory named myDirectory.
The hub.txt file intuitively sets the configurations like the hub name and the genome configureation file (genomes.txt) for the track hub.
hub my_hub
shortLabel my hub short label
longLabel my hub longer label
genomesFile genomes.txt
email [email protected]
In the below example the track hub is for hg19 and the information about custom tracks can be found in the trackDb.txt file in the myDirectory folder.
genome hg19
trackDb myDirectory/trackDb.txt
To display multiple wigs in one track, you need to specify a track as having a container of "multiwig". Then in subsequent sub-track definitions point to the multiwig track as the parent of that sub-track. You may have many "multiwig" custom tracks in your track hub, it is not limited to one. You can edit the parameters for the track to get exactly what you want.
track brain
container multiWig
shortLabel My Brain Data
longLabel My Brain Data
type bigWig 0 30000
viewLimits 0:100
visibility full
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
windowingFunction mean
priority 1.4
configurable on
autoScale on
track brain1
bigDataUrl brain1.bw
shortLabel brain1_data
longLabel brain1_data
parent brain
type bigWig
color 125,0,0
track brain2
bigDataUrl brain2.bw
shortLabel brain2_data
longLabel brain2_data
type bigWig
parent brain
color 0,125,0
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Click on the My Hubs tab
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Paste your url into text entry. It may look something like the following if you are using ftp:
ftp://userName:[email protected]/myDirectory/hub.txt -
Click the Add Hub button
If you run into issues, you can check the official documentation at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.