Question regarding creation of track hubs with nested folders

[Nowlan Freese]

We are trying to create a track hub that contains nested folders. For example, a top level folder would be for our project, a subfolder for the sample which contains different data types such as bam, bigBed, and bigWig. As far as we can figure out we can create a top level folder using a "supertrack". But we cannot figure out how to create subfolders. Is this possible? 

Thank you

Nowlan

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Nowlan Freese, PhD | Research Assistant Professor
UNC Charlotte | Bioinformatics and Genomics
150 North Research campus Dr | Kannapolis, NC 28081
nfreese@charlotte.edu | charlotte.edu

[Luis Nassar]

Hi, Nolan.

We have two kinds of containers, supertracks and composite tracks.

• Supertracks: Meant to be general folders unifying a theme or project, meaning the data types inside can vary. One example is ENCODE3 Regulation (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg) which contains all sorts of data inside.
• Composite tracks: Designed to group together tracks of the same type. For example, many different RNA-seq bigWig signals from different GTEx tissues (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=gtexCov).

It is worth noting that you can use the API to find the trackDb of any of these tracks, e.g.

https://api.genome.ucsc.edu/list/tracks?genome=hg38

gtexCov    
compositeContainer    "TRUE" 
shortLabel    "GTEx RNA-Seq Coverage" 
type    "bigWig" 
longLabel    "GTEx V8 RNA-Seq Read Coverage by Tissue" 
maxHeightPixels    "100:50:8" 
group    "expression" 
compositeTrack    "on" 
priority    "10.20" 
autoScale    "group" 

The last important note is that composites can be inside of a supertrack (but not inside other composites), but supertracks cannot be nested in anything. So the deepest level you could organize would be supertrack -> composite -> tracks. There is one niche exception: if you want to have a combination of bigBeds and bigWigs inside a composite, you can use views (https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#view), for example, RNA-seq signals and peaks both in one container.

We are working on a new hubs basic page, currently only on our development server: https://genome-preview.soe.ucsc.edu/goldenPath/help/hubBasics.html#grouping.

So to answer your question, yes, you are looking to make a supertrack, and inside that supertrack you can add individual bigBeds/bigWigs, or additional composites with their own tracks inside. The grouping example above has a template.

Let us know if you have any questions or suggestions on this content.

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Lou Nassar
UCSC Genomics Institute

[Nowlan Freese]

Thank you Luis!

On Wed, Nov 5, 2025 at 4:52 PM Luis Nassar <lrna...@ucsc.edu> wrote:

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