Question: How To Create 'Grass-Like' Graphs (Barcharts) In Ucsc Browser Tracks?
4
gravatar for Giovanni M Dall'Olio
9.9 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

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

alt text

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.: alt text

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?

bed visualization ucsc • 2.3k views
ADD COMMENTlink modified 9.9 years ago by Ryan Dale4.9k • written 9.9 years ago by Giovanni M Dall'Olio27k
1

I will now forever call them grass graphs haha

ADD REPLYlink written 9.9 years ago by Sequencegeek740

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

ADD REPLYlink written 9.9 years ago by Giovanni M Dall'Olio27k
8
gravatar for Mary
9.9 years ago by
Mary11k
Boston MA area
Mary11k wrote:

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

ADD COMMENTlink modified 9.9 years ago • written 9.9 years ago by Mary11k
5
gravatar for Casey Bergman
9.9 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

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.

ADD COMMENTlink written 9.9 years ago by Casey Bergman18k

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

ADD REPLYlink written 9.9 years ago by Giovanni M Dall'Olio27k
5
gravatar for Ryan Dale
9.9 years ago by
Ryan Dale4.9k
Bethesda, MD
Ryan Dale4.9k wrote:

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

ADD COMMENTlink written 9.9 years ago by Ryan Dale4.9k

thanks, I will need it.

ADD REPLYlink written 9.9 years ago by Giovanni M Dall'Olio27k
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