Tutorial:Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]

Question

[Sukhi Singh]

Hi, just wrote a quick tutorial for overlaying multiple tracks in ucsc.

Follow the link http://biofeed.tumblr.com/post/45676161703/overlay-multiple-tracks-in-ucsc-browser.

For full documentation and detailed syntax refer to

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

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

[brianpenghe]

Your tumblr link no longer works

[Theodore Pak]

Hey Sukhdeep, if you work with a lot of custom tracks in UCSC formats I'm curious what you might think of http://chromozoom.org . It's a genome browser that I wrote that basically makes moving around UCSC-rendered genomes very fast and easy. Perhaps you might find it useful, or have some feedback.

Of course it does not support some of the more complicated features of UCSC yet, like track hubs, but it hold some value for quick sharable visualizations of wig/bed/big{Wig|Bed} tracks.

[Sukhi Singh]

Hi Theodore, Its a super application. Very beautiful use of HTML5. Ofcourse, you will be having some addons on your to do list, but Its very fast as a minimal browser and navigation is super. Just few things,

• Could you add other genomes like mm10 etc.

• Can we have different visualization options for the bigwig, right now its histogram, so may be peaks (slopes), points, heatmap etc.

• Can you add more annotation tracks like CpG island by default (other way would be to import them via bed).

Anyway, its great :)

[fr]

Hi, I have generated two tracks, one with positive and the other with negative scores. My idea was to overlay them and thus you see on the same track some values being negative and others positive. I have successfully overlaid them, but both end up showing as positive and the scale allowed is only 0 - 127. Do you have any suggestions for this?

Edit: I see now that while you cannot change the vertical viewing range to include negative values as well, setting it as "autoscale to data view" shows both positive and negative values. Not ideal though...