Wednesday, November 28, 2012

How to modify properties of wig custom tracks in UCSC Genome Browser

If you uploaded wig file as a custom track in UCSC and you want to modify the properties of it do the following.
When in the Genome Browser click on the Manage custom tracks bellow, then click on the wig track you want to modify.
Enter for example:

track type=wiggle_0 name="NSC_H2AU_vs_IgG_control_all" smoothingWindow=4 description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp" color=123,100,50 autoScale=off viewLimits=1:20 visibility=full windowingFunction=maximum

name="", name of the track displayed on the side of the Genome browser
description="", name of the track displayed on the top of the track
color=x,y,z, color of the track in RGB decimal values

See this link for the examples of colors and their respective RGB decimal values:
http://en.wikipedia.org/wiki/Web_colors

autoScale=off, set the autoscale off if you want to compare different tracks, otherwise each track will be set to its own scale
viewLimits=1:x, set the view limits for the track, keep this the same for different wig files if you want to compare them
visibility=full, set to full to expand the track, otherwise put dense
windowingFunction=maximum, when the individual data points of the wig file cannot be presented in the plot, then UCSC will combine the nearby values to produce a plot point. Set this to maximum, mean, minimum, or mean+whiskers.
smoothingWindow=4, number of the pixels of the smoothing window that will pass over the plot to smooth the edges of the peaks

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