Displaying Different Sized Lines In Ucsc Genome Browser

Question

[firedreamer]

I'm new to using the UCSC genome browser, and I'm making a custom track of SNPs where I'd like the height of my track lines to vary based on a value I specify for each range. Is this possible? Also, would it be possible to display the SNPs as dots instead of lines?

Answer 1

[Sukhi Singh]

Right click on individual tracks and then play with these parameters.

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

[firedreamer]

Thanks, but right clicking on the tracks only gives me the options hide, dense, squish, pack, and full, which doesn't really do what I want. I was hoping for a way to specify, preferably in the custom track file, the height of each line indicating a SNP--a different height for each one, even though they are in the same data group.

[John St. John]

Yea, not sure if you can do this in custom tracks or not. Try right clicking on one of the default tracks, you should see an option "Configure ..." near the bottom of the drop down that comes up when you do that. Just tried this.

[Sukhi Singh]

You need to click on the second last option named as "Configure " appended with your track name or if you have bigwig's, your parameter settings can be controlled from your track file.

See Visualizing Chip-Seq data using UCSC [Bigwig]