Custom Tracks: setting a vertical viewing range in a track file

[David Leader]

I am developing a web app in which, after a search for a particular gene, in addition to a table of results a link will be provided so that the RNAseq data for a gene (bigWIg format) can be viewed in the UCSC browser.

I am doing this following Example 11 on http://genome-euro.ucsc.edu/goldenPath/help/customTrack.html and am using a text file on my own server with multiple tracks. This is working well, and I have been able to specify colour, max pixel height (32px) and display-type on the "track".

As I am showing multiple tracks (from different drosophila tissues) I do not want them to autoscale to fit my 32px, but to use the same absolute scale so the viewer is not misled by weak signals. I have managed to do that *interactively* in the dialog box using:

Data view scaling: "use vertical viewing range setting"

Vertical viewing range: min: 1 max:1500 (or whatever)

but I can't see how to add these settings to the track in my text file. I've looked at:

http://genome-euro.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html#wig_-_Signal_Graphing_Track_Settings

and tried various things, but to no effect.

Is it possible? Am I missing something obvious.

David

_______________________________________________________

Dr. David P. Leader (Honorary Research Fellow)

College of Medical, Veterinary & Life Sciences,

University of Glasgow, Glasgow G12 8QQ, UK

Phone: +44 (0)141 330 5905 

http://www.davidleader.net

The University of Glasgow, charity number SC004401

_______________________________________________________

[Hiram Clawson]

Good Morning Dr Leader:

You can use the 'viewLimits' variables to set an absolute
viewing range. You must also set 'autoScale off' to turn off
the auto scaling.

--Hiram

[Hiram Clawson]

A 'bigWigInfo yourFile.bw' can tell you the range of data in the bigWig file.

--Hiram

On 2/12/14 8:56 AM, David Leader wrote:
> Thanks Hiram.
>
> Adding autoScale=off viewLimits=1:1500 did the trick for the particular gene I was looking at.
> I guess if I'd thought about it a bit more I'd have realized I needed to set two switches as in the dialogue box.
>
> Easy enough to hard-code but I don't see how I'll be able to find the max peak height dynamically, now I come to think of it.
>
> Oh well...
>
> David

[David Leader]

Thanks Hiram. 

Adding autoScale=off viewLimits=1:1500 did the trick for the particular gene I was looking at.

I guess if I'd thought about it a bit more I'd have realized I needed to set two switches as in the dialogue box.

Easy enough to hard-code but I don't see how I'll be able to find the max peak height dynamically, now I come to think of it.

Oh well...

David

On 12 Feb 2014, at 4:28pm, Hiram Clawson wrote: