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diff --git a/topics/adding-bigwig-track.gmi b/topics/adding-bigwig-track.gmi new file mode 100644 index 0000000..19b0364 --- /dev/null +++ b/topics/adding-bigwig-track.gmi @@ -0,0 +1,46 @@ +# 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 |