Adding Quantitative Tracks Using BigWig Files

Setting up JBrowse2

Install and Serve JBrowse2

npm install -g @jbrowse/cli jbrowse create jbrowse2 cd jbrowse2 npx serve -s .

This command first installs jbrowse's cli, which is essential for creating and managing jbrowse2 instances, and then creates a jbrowse2 project. After that, we cd into it and serve it using npx. Our instance of jbrowse2 can now be accessed at

Creating and Loading a BigWig track

Cleaning wig files

Remove any existing track or browser lines from the wig files

Create chrom.sizes files for the database

Use the fetchChromSizes binary to create chrom.sizes files for the existing wig files

fetchChromeSizes binary location

Converting wig files into a bigWig file

wigToBigWig input.wig chrom.sizes bigWig.bw

The wigToBigWig binary can be used to convert wig files into the bigWig format. The bigWig format provides a more efficient way to view larger wig files, as only the sections being displayed are rendered to the screen.

wigToBigWig binary location

Adding the bigWig track

jbrowse add-track bigWig.bw --load copy --out /var/www/html/jbrowse

Where /var/www/html/ is the static HTML folder of the web server

Adding it to the custom track management page

You can then open it from Add Track and passing the URL

Alternative way to add it

You can open the "Add Track" menu, choose the bigwig file and load it

Customizing the track

Clicking on the "???" next to the file name and clicking on settings opens a settings menu, where multiple traits such as the track name, description et cetera can be modified.

Setting up the Quantitative View

Getting whole-genome CNV coverage

Click on the ??? symbol on the top left corner of the view
Click on "Show" and click on "Show all assembly lines"
Now, click on the �� next to the bw file name in the view
Click on Fill mode -> no fill
Click on Score -> Autoscale type -> Local + 3��
Click on Score -> Resolution -> Finer resolution
Repeat the finer resolution step a couple of times