UCSC Genome Browser custom overlap tracks

One of the features of the latest update to the UCSC Genome Browser (see http://www.ncbi.nlm.nih.gov/pubmed/20959295), are tracks which overlap or overlay each other. If you’re a regular user of the site, you will have noticed the ENCODE ChIP-Seq tracks that have several layers. After doing a bit of searching, I was able to make my own overlapping tracks. Since it’s a new feature, there is yet to be official documentation on it. But several users have emailed the mailing list regarding this and if you join up the bits and pieces, you can piece together the instructions for making your own custom overlap tracks.

Things you require are access to a web server, and knowledge of making bigWig files. See this post on how to make bigWig files from BAM files. If you have those, next you need to set up your own track hub; follow the official instructions on how to do this.

Once you have setup your track hub and debugged it using hubCheck tool, adapt the following attributes shown below to your own trackDb.txt file. See this thread for more information.

For my example, I made two bigWig files and I wish to overlap them together as one track. So in my trackDb.txt file, I have something like this (pay attention to the lines in bold):

track all_fun
container multiWig

shortLabel all_fun
longLabel all_fun
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 fun
bigDataUrl fun.bw
shortLabel fun
longLabel fun
parent all_fun
type bigWig
color 180,102,255

track fun2
bigDataUrl fun2.bw
shortLabel fun2
longLabel fun2
type bigWig
parent all_fun
color 136,102,255

The key is to make a container track (which I named all_fun), and for every track that you want to overlap, specify the same container name in the parent field (I have put them in bold above).

For more information on the track attributes have a look at Jim Kent’s git hub and the official documentation on wiggle tracks.

Next, the UCSC Genome Browser needs to make it possible to properly display bedGraph files when reads are mapping to the exact same position but on opposite strands. UPDATE 22nd March 2012: As suggested by Xianjun (see comments for this post), to solve the issue of displaying +/- reads that map to the same spot, create two bigWig files, one for the plus strand and the other the minus, and just overlay those into one track as shown above. Worked like a charm.

For more information see http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html.

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6 comments Add yours
  1. Thanks for the tips.

    For your last point, I am wondering you can just generate a bedGraph file for each strand, and set the values on ‘- ‘strand as negative, then generate bigwig files for them, then display the two files in your subtrack way.

  2. Have a question on this,
    I made the trackDb.txt and when I put the path (ftp) to that in the “Add Custom Tracks” and submit it, I am getting ” line 1 of var A21771 in custom input: A21771 missing = in var/val pair”. any thought on that?

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