UCSC Viewer : Adjust all tracks on the same scale at the same time.

Question

[ZheFrench]

Question is in the title. Imagine you have many bigwig track...and you want to display the same scale for each tracks but you don't want to change viewlimits one by one for all of them. Is there a way to do that in a one time shot for all using maybe session file or Supertrack ,multiwig, composite arguments.

[GenoMax]

While someone may answer these UCSC specific question here you may also want to post them to UCSC browser forum at [e-mail]

Answer 1

[Rashedul Islam]

You can check the "Oct. 11, 2019 New "group auto-scale" option" here.

Example track file for group of tracks: bigWig

track myComposite  
compositeTrack on  
shortLabel test 
longLabel my_comp_testing
type bigWig  


    track myFirstSubtrack
    parent myComposite on
    shortLabel test_1_short
    longLabel tes_1_long
    type bigWig
    visibility full
    maxHeightPixels 70:70:32
    configurable on
    autoScale off
    viewLimits 0.0:1.0
    alwaysZero on
    priority 0.1
    bigDataUrl file1.bw
    color 0,0,0


    track mySecondSubtrack
    parent myComposite on
    shortLabel test_2_short
    longLabel tes_2_long
    type bigWig
    visibility full
    maxHeightPixels 70:70:32
    configurable on
    autoScale off
    viewLimits 0.0:1.0
    alwaysZero on
    priority 0.1
    bigDataUrl file2.bw
    color 0,0,255

```

Answer 2

[Ian]

You cannot do this using a normal set of custom tracks. You will need to implement a trackhub. Two useful references are:

• Primary UCSC help http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

• Track database definition doc http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

Using trackhubs allows you to group data together. You can also select samples based on custom cateorgies, such as replicate, ChIP, input, tissue, etc.

Lots of examples can be seen at: https://genome-euro.ucsc.edu/cgi-bin/hgHubConnect

If you click on the hub name you can look at the necessary files. BTW to use trackhubs you need access to a web-server.

[Maximilian Haeussler]

Ian, can he really set the view limits globally if he uses a track hub composite?

[Maximilian Haeussler]

Oh sorry, this is probably more the multiWig mode rather than the composite... nevermind... https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#multiWig