# 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
=> https://localhost:3000 

## 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
=> http://hgdownload.soe.ucsc.edu/admin/exe/ 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.
=> http://hgdownload.soe.ucsc.edu/admin/exe/ 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 + 3α
* Click on Score -> Resolution -> Finer resolution
* Repeat the finer resolution step a couple of times