Question: UCSC hub: autoscale option for multiwig track
0
gravatar for m93
8 months ago by
m93150
m93150 wrote:

I am making a hub on UCSC Genome Browser and I am aiming to display multiple bigWig files as a single track (multiwig container). I decided to use the autoscale option because I wanted a dynamic scale: y axis changing depending on the maximum values in the current observed window.

However, I am confused as to how to the relationship between:

  • autoscale on and viewLimits
  • autoscale on and type bigWig <#> <#>

For the "type" option, the official documentation mentions that: "The remote data files of type bigWig must declare the expected signal range for the data"

So my question is, are the following assumptions correct:

  • If I have autoscale on, viewLimits and type don't really matter anymore
  • You still have to specify "type bigWig" but you no longer have to put a range (i.e. the <#> <#>)
  • You don't have to viewLimits.

If this is correct, my trackDb.txt file will look as such::

track data
container multiWig
configurable on
shortLabel label data
longLabel long label data
visibility full
priority 1
type bigWig
autoScale on
aggregate transparentOverlay
windowingFunction mean
showSubtrackColorOnUi on

    track sample1
    bigDataUrl path/to/sample1.bw
    shortLabel s_sample1
    longLabel s_sample1
    type bigWig
    visibility full
    alwaysZero on
    priority 120
    color 220,180,180
    parent data on

    track sample2
    bigDataUrl path/to/sample2.bw
    shortLabel s_sample2
    longLabel s_sample2
    type bigWig
    visibility full
    alwaysZero on
    priority 120
    color 220,180,180
    parent data on

    etc
ucsc track autoscale multiwig • 293 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by m93150
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1477 users visited in the last hour