Making a hub for a cell browser

This page will go over how to use the makeCbHub script to build a track hub from bigWig, bigBed, and other big* files provided by a submitter.

File organization

The script assumes a certain directory structure when it creates the trackDb stanzas.

In your dataset directory, create a ‘hub’ directory where all of the hub-related files will live. In that hub directory, you will then create a directory for each composite/parent track (directory names should be all lowercase):

cb_dataset_dir/
    |--> hub/
        |--> track_set_A/
            |--> track_A1.bw
            |--> track_A2.bw
            |--> etc…
        |--> track_set_B
            |--> track_B1.bw
            |--> etc…

Dividing the individual tracks into composite/parent tracks will vary from dataset to dataset. For example, in the collection mouse-brain-cutandtag, individual tracks were divided into a composite track for each dataset in the collection (e.g. h3k27ac, h3k27me3, h3k27me3-cell-lines, h3k36me3, h3k4me3, olig2, rad21) as this was what was requested by the authors. In neuro-degen-atac, individual tracks were grouped according to their corresponding metadata field (e.g. broad-celltypes, clusters, neuronal-celltypes, neuronal-clusters). If you’re not sure how to group the tracks ask Max and/or the contributors.

Finally, it’s best to make symlinks to the track files in the orig directory to prevent the unnecessary duplication of large amounts of files. See human-enhancer-atlas/hub and fetal-chromatin-atlas/hub as examples, where the bigWigs alone were 212 GB and 138 GB, respectively. (/hive has a ton of storage, but it's good to not waste space unnecessarily.)

Running the script

For makeCbHub, at the very least, all you need is a directory of big* files. This is the required argument fileDir.

For example, use the commands below to generate the trackDb stanzas for a single composite track in the mouse-brain-cutandtag dataset:

cd /hive/data/inside/cells/datasets/mouse-brain-cutandtag/hub
makeCbHub olig2

Output:
track olig2
compositeTrack on
shortLabel olig2
longLabel olig2
visibility dense
autoScale group
type bigWig

     track olig2_cluster_non_oligo
     parent olig2 on
     shortLabel cluster_non_oligo
     longLabel cluster_non_oligo
     type bigWig 0.000000 2358.294189
     autoScale group
     bigDataUrl olig2/cluster_non_oligo.bw
     visibility dense

     track olig2_cluster_oligo
     parent olig2 on
     shortLabel cluster_oligo
     longLabel cluster_oligo
     type bigWig 0.000000 280.645325
     autoScale group
     bigDataUrl olig2/cluster_oligo.bw
     visibility dense

As you can see, it works, though it wouldn't be particularly pretty to look at the Genome Browser. The labels are not very human-friendly and both tracks will be colored the same, default color, black.

Options to customize output

The six optional arguments for makeCbHub allow you greater control over what’s put into these trackDb stanzas, including shortLabels, longLabels, and colors.

Composite track labels

The option -d/--datasetList serves two purposes:

1. If fileDir contains multiple dirs, you can specify which of those you want to build trackDb stanzas for
2. By default, the directory names under fileDir are used as the labels for the composite/parent tracks in the trackDb. However, these are required to be all lowercased (e.g. h3k27ac, bw, or clusters). This option allows one to specify the casing used for the short/long labels.

makeCbHub -d “Rad21 Olig2” bw/

track rad21
compositeTrack on
shortLabel Rad21
longLabel Rad21
visibility dense
autoScale group
type bigWig
...

track olig2
compositeTrack on
shortLabel Olig2
longLabel Olig2
visibility dense
autoScale group
type bigWig
...

This command assumes that in bw/ (fileDir), there are two directories: rad21 and olig2, but it will use Rad21 and Olig2 as the shortLabel/longLabel for those composites in the trackDb.

Individual track labels

The options -s/--shortLabel and -l/–longLabel allow you to control the short and long labels of the individual tracks in the composites. By default the script uses the file names as the labels, which, depending on how the files are named, can be pretty messy:

cd /hive/data/inside/cells/datasets/olg-eae-ms/eae-multiomics/hub
makeCbHub bw/

Which results in:

    ...
    track bw_P21208_1004_OPC_Ctr_RND1_peaks
    parent bw on
    shortLabel P21208_1004_OPC_Ctr_RND1_peaks
    longLabel P21208_1004_OPC_Ctr_RND1_peaks
    type bigWig 0.000000 160.000000
    autoScale group
    bigDataUrl bw/P21208_1004_OPC_Ctr_RND1_peaks.bw
    visibility dense
    ...

However, if we rebuild the trackDb with these options:

cd /hive/data/inside/cells/datasets/olg-eae-ms/eae-multiomics/hub
makeCbHub -s shortLabels.tsv -l acronyms.sorted.tsv bw/

Which outputs:

    ...
    track bw_P21208_1004_OPC_Ctr_RND1_peaks
    parent bw on
    shortLabel OPC_Ctr
    longLabel OPC_Ctr - Control oligodendrocyte precursor cells
    type bigWig 0.000000 160.000000
    autoScale group
    bigDataUrl bw/P21208_1004_OPC_Ctr_RND1_peaks.bw
    visibility dense
    ...

The shortLabels file contains two columns.

1. file name
2. short label

Here's the line from the shortLabels.tsv used in the example above:

P21208_1004_OPC_Ctr_RND1_peaks.bw       OPC_Ctr

The longLabels file follows the same format as the 'acronymFile' setting that can be specified in the cellbrowser.conf (and will mostly likely be the same file). The two columns are:

1. short label
2. long label

Here's the line from the acronyms.sorted.tsv used in the example above:

OPC_Ctr Control oligodendrocyte precursor cells

Note: the shortLabel/longLabel files can be csv or tsv format and their file names need to end with csv or tsv (e.g. shortLabels.tsv).

Colors

If a track doesn't include the 'color' setting, the Genome Browser colors that track black by default. The -c/–color option allows you to specify the color for each track. The file follows the same format as the 'colors' setting that can be specified in the cellbrowser.conf (and will mostly likely be the same file). The two columns are

1. short label
2. hexcode color (e.g. #834088), although RGB tuples (e.g. '131 64 136' or '131, 64, 136') are also accepted

Using all these together

Altogether, those three options will result in a pretty solid track hub. Here's a example you can run to see the results yourself:

cd /hive/data/inside/cells/datasets/olg-eae-ms/eae-multiomics/hub
makeCbHub -s shortLabels.tsv -l acronyms.sorted.tsv -c ../colors.csv bw/

Which gets us:

    ...
    track bw_P21208_1004_OPC_Ctr_RND1_peaks
    parent bw on
    shortLabel OPC_Ctr
    longLabel OPC_Ctr - Control oligodendrocyte precursor cells
    type bigWig 0.000000 160.000000
    autoScale group
    color 131,64,136
    bigDataUrl bw/P21208_1004_OPC_Ctr_RND1_peaks.bw
    visibility dense
    ...

View it in the Genome Browser and take a look at the hub.txt used for that hub: https://cells.ucsc.edu/olg-eae-ms/eae-multiomics/hub/hub.txt.

Track description page

Additionally, you'll need to create a track description page for the hub. A track description page describes the data that people are looking at, any display conventions to keep in mind for that data (e.g. coloring), a contact email, and a reference to the paper(s). If you keep the page fairly high-level, you can use the same one for all of the tracks in the hub. Even if there are multiple composite/parent tracks in your hub, you can use the same description page for all of them since often the data are very similar.

You can use the Genome Browser template as a starting point. Additionally, it can be useful to look at the track description pages for other hubs in the Cell Browser:

• olg-eae-ms/eae-multiomics: https://cells.ucsc.edu/olg-eae-ms/eae-multiomics/hub/track_desc.html
• olg-eae-ms/eae-atac: https://cells.ucsc.edu/olg-eae-ms/eae-atac/hub/track_desc.html
• neuro-degen-atac dataset: https://cells.ucsc.edu/neuro-degen-atac/track_desc.html (A good example of covering multiple composites with one page)

Once you have the page written, place it in the hub/ directory and use cbMakeHub to add the proper settings to the trackDb stanzas:

cd /hive/data/inside/cells/datasets/olg-eae-ms/eae-multiomics/hub
makeCbHub -s shortLabels.tsv -l acronyms.sorted.tsv -c ../colors.csv -f track_desc.html bw

Which outputs:

track bw
compositeTrack on
shortLabel bw
longLabel bw
visibility dense
autoScale group
type bigWig
html track_desc.html

     track bw_P21208_1004_OPC_Ctr_RND1_peaks
     parent bw on
     ...

Getting the hub ready

Using makCbHub is just part of the process in getting your hub ready. This section will step through the process of making a hub and getting it to show up for a cell browser. It assumes that your hub only covers one genome assembly (e.g. mm10 or hg38), not multiple. If a track hub only covers one assembly, you can take advantage of the setting 'useOneFile on' to put everything into a single hub.txt file. Hubs on multiple assemblies are a little more complex and require a set of hub.txt/genomes.txt/trackDb.txt files.

Common hub.txt settings

These settings will show up in any hub you create for the Cell Browser, though you will need to adjust the settings according to be specific to your hub:

hub eae_multiomics
shortLabel scATAC-seq of EAE Mice
longLabel scATAC-seq of EAE Mice
genomesFile genomes.txt
email eneritz.agirre@ki.se
descriptionUrl https://www.sciencedirect.com/science/article/pii/S0896627321010898
useOneFile on

genome mm10

Breakdown of what to do for each setting in the first stanza:

• hub - can be the same as the dataset short name (e.g. neuro-degen-atac)
• shortLabel and longLabel - can be the same, though feel free to add more details to the longLabel if needed
• genomesFile - will always be genomes.txt
• email - should be the email of the contributor
• descriptionUrl - can point to the paper or to the track description page you created
• useOneFile - will always be on

After that, there should be a line break and then the 'genome' setting. You will need to confirm with the contributor about what genome assembly they aligned their data to. If it's a public dataset, you may be able to find this information in the methods section.