Overlay Multiple Tracks in UCSC Browser
Guys, a quick tutorial on how to overlay multiple tracks in UCSC genome browser.
If you are acquainted with how to visualize your NGS data with UCSC, then move forward with this tutorial, else read this post first. [http://biofeed.tumblr.com/post/45142855966/visualizing-chip-seq-data-using-ucsc]
You will need a publicly accessible web-server, bigwig files and a text editor.
Fire up the text editor, and make a file called hub.txt.
We will make Track hubs, from the official page of UCSC
Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Hubs are a useful tool for visualizing a large number of genome-wide data sets. For example, a project that has produced several wiggle plots of data can use the hub utility to organize the tracks into composite and super-tracks, making it possible to show the data for a large collection of tissues and experimental conditions in a visually elegant way, similar to how the ENCODE native data tracks are displayed in the browser.
This will be your control file for navigating the tracks as hubs.
My hub.txt contains the following lines:
https://gist.github.com/vanbug/5187385
where hub is followed by the parent directory name, which will contain all the tracks and this text file (hub.txt) genomesFile will contain the information about which genomes are required to view the files for on UCSC. They should be standard UCSC annotations like mm9,mm10,hg18 etc. Rest of the fields are self-explanatory and required. Now, create another text file called genomes.txt, which should have
genome mm10 trackDb mm10/trackK4Db3.txt
where genome is the genome to which I mapped my files
and trackDb is the trackDb file which contains the information about your tracks
Now, make a directory inside your parent directory. Lets call it mm10.
Inside this directory, make another text file called trackK4Db3.txt, as declared earlier.
My trackDb file has these entries
https://gist.github.com/vanbug/5187466
The first para is the parent container, lets call it major. It will contain all the information about the display of child tracks. You can set the options like viewLimits,windowingFunction etc. type is really important parameter, telling about the type of your file (bigwig in this case)
Follows then the information about each track which will be contained under this parent container.
Like this first one in H3K4me3, bigDataUrl will have the location of the file, it can be a hyperlink/ftp or simply the file location.
parent parameter conveys the container information.
Another important parameters in the parent container are the
>aggregate transparentOverlay showSubtrackColorOnUi on
Now, with all set, we will give the port in the url of the hub file to the UCSC.
As we are taking about mm10 here, so append the url of the hub file to this url, http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&hubUrl=
So, the final url is http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm10&hubUrl=https://sukhdeeps_webdav/hub.txt
This will produce the following pretty image
Small Trick : Adding cpgIslandExt=pack to the url with switch on the cpg islands.
Cheers