f49623d03093fdc8e7f06b65abb0b77efad6a3b9 Merge parents bbabbd5d256 7ec5fd8d353 mspeir Sun Oct 26 12:19:55 2025 -0700 fixed merge conflict. diff --cc src/hg/htdocs/goldenPath/help/hubBasics.html index 9ddd7a5821a,19df6a02d91..e09ea0f79b0 --- src/hg/htdocs/goldenPath/help/hubBasics.html +++ src/hg/htdocs/goldenPath/help/hubBasics.html @@@ -68,69 -68,70 +68,76 @@@ # shortLabels should be under 20 characters and longLabels under 70 shortLabel Example Hub longLabel Example Hub for useOneFile option useOneFile on email genome-www@soe.ucsc.edu genome hg38

If you have tracks across multiple assemblies, see the full track hub documentation.

Common Track Types

- The most common track types are bigBed and bigWig, compressed, binary versions of - corresponding plain-text formats. Together they should cover much + The most common track types are bigBed and bigWig. Compressed, binary versions of + the corresponding plain-text formats. Together they should cover most of what you might want to display in the Genome Browser, from transcription peaks to - RNA-seq results. + RNA-seq signals.

bigBed Tracks

You can use bigBed tracks to display discrete annotations, such as genes, transcription start sites, or conserved genomic elements. The bigBed format builds off the plain-text BED format and is thus flexible in terms of what fields are included. - Your file must start with a set of 12 standard fields (though not necessarily all of them), but + Your file must start with a minimum of 3, and up to 12, standard fields, but can also extend the format with any number of additional fields.

Building a bigBed

- Next, we'll discuss how to build a bigBed from a bed file.

Download the bedToBigBed utility for your system type from - our download + our download server.
Use bedToBigBed to build your bigBed:
```
bedToBigBed -sort in.bed chrom.sizes myBigBed.bb
```
- If your assembly is a UCSC-hosted assembly (e.g. hg38), chrom.sizes can ++<<<<<<< HEAD + be a URL (replace "genNom" with the assembly name (e.g. hg38)): + http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. + If you're working with a GenArk assembly hub, then the chrom.sizes ++======= + be a URL (e.g. hg38): + + https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes. + If you're working with a + GenArk assembly hub (e.g. GCF/GCA), then the chrom.sizes ++>>>>>>> 7ec5fd8d353ae3486915167a5d57c84cb0cb918f file can be found under the "Data file downloads" section on the assembly gateway page.
- If you have custom fields in your bed file, you will need to create a custom .as file. You can download the basic BED .as and modify this by adding new fields below those in your file.
Put your bigBed file alongside your hub.txt in a web-accessible location, either through the 10GB of space we make available to users or through one of several - other services -
You will use the file name (e.g. "myBigBed.bb") with the bigDataUrl setting in your hub.txt + other services. +
You will use the file name (e.g. "myBigBed.bb") with the bigDataUrl setting in your hub.txt.

bigBed track hub configuration

Once you have built your bigBed files, it is time to create a stanza in your hub.txt file for that track. Here is what the required settings discussed above might look like for a basic bigBed track:

track bigBedRequiredSettings
  shortLabel bigBed Required Settings
  longLabel A bigBed Example with Required Settings
  visibility pack
  type bigBed 12 +
  bigDataUrl gtexCaviar.chr7_155799529-155812871.bb

@@@ -174,63 -177,64 +183,64 @@@

And here is what that track looks like in the Genome Browser:

These common settings added options to the track configuration pop-up:

bigWig Tracks

You can use bigWig to tracks to display continuous annotations, such as RNA-seq expression, conservation scores, or other - genome-wide scores. You can build a bigWig using one of two plain-text formats: + genome signal scores. You can build a bigWig using one of two plain-text formats: wiggle or bedGraph.

Building a bigWig

- Next, we'll discuss how to build a bigWig from a wig or bedGraph file.

Download the wigToBigWig utility for your system type from - our download + our download server.
Use this utility to build your bigWig:
```
wigToBigWig in.bedGraph chrom.sizes myBigWig.bw
```
- If your assembly is a UCSC-hosted assembly (e.g. hg38), chrom.sizes can - be a URL (replace "genNom" with the assembly name (e.g. hg38)): - http://hgdownload.gi.ucsc.edu/goldenPath/genNom/bigZips/genNom.chrom.sizes. - If you're working with a GenArk assembly hub, then the chrom.sizes + be a URL (e.g. hg38): + + https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes. + If you're working with a + GenArk assembly hub (e.g. GCF/GCA), then the chrom.sizes file can be found under the "Data file downloads" section on the assembly gateway page.
Put your bigWig file alongside your hub.txt in a web-accessible location, either through the 10GB of space we make available to users or through one of several - other services -
You will use the file name (e.g. "myBigWig.bw") with the bigDataUrl setting + other services. +
You will use the file name (e.g. "myBigWig.bw") with the bigDataUrl setting.

bigWig track hub configuration

The basic trackDb configuration for a bigWig track is similar to a bigBed track as - all tracks required the same basic settings (track, shortLabel, longLabel, type, bigDataUrl). + all tracks require the same basic settings (track, shortLabel, longLabel, type, bigDataUrl). This is what the configuration for a bigWig track might look like (the example hub.txt includes other useful settings):

track bigWigExample
  shortLabel bigWig Example
  longLabel A bigWig Example with Commonly Used Settings
  visibility pack
  type bigWig -20 10.003
  bigDataUrl hg38.phyloP100way.chr7_155799529-155812871.bw
  color 60,60,140

The type line consists of two parts:

"bigWig" is the basic track type
"-20 10.003" indicates the minimum and maximum of the data in the bigWig