How To Create 'Grass-Like' Graphs (Barcharts) In Ucsc Browser Tracks?

Question

[Giovanni M Dall'Olio]

Some of the tracks in the UCSC browser are shown as spiky or 'grass-like' charts:

I can not find the documentation on how to create these kind of graphs. In the User Track documentation, there is the description of BED and GFF files; However, it seems that these can only be represented with different colors.

For example, the documentation for the 'score' attribute in BED doesn't say anything about the height of the ticks to be represented.:

How can I define the height of the ticks in a custom track for the UCSC browser? Which format should I use, BED, GFF or another?

[Sequencegeek]

I will now forever call them grass graphs haha

[Giovanni M Dall'Olio]

@sequenceGeek: eheh fine, they are just barcharts :-)

Answer 1

[Mary]

That's a WIG track, or sometimes a BigWig track. There's a reference specifically about BigWig, let me get that, brb.

Here's a page on Wiggle: http://genomewiki.ucsc.edu/index.php/Wiggle But there was another one that I found helpful, still looking.

And there's these: BigWig and BigBed: enabling browsing of large distributed datasets

Answer 2

[Casey Bergman]

I think what you are looking for is the Wiggle format, which allows the display of continuous data. When zoomed out you see the peaks among the background.

[Giovanni M Dall'Olio]

thanks you both!! I figured out a bit after posting the question... it is true, it is a Wiggle format.

Answer 3

[Ryan Dale]

Once you make WIG files, here's a step-by-step tutorial on how to convert your WIG files to bigWig format, which is very useful for large data sets:

http://genome.ucsc.edu/goldenPath/help/bigWig.html

[Giovanni M Dall'Olio]

thanks, I will need it.