III – Extensions

Here we discuss more advanced usage, exchanging tracks with other genome browsers.

Table of contents

III - Extensions
  III-1. Using CeNGEN tracks in other genome browsers
  III-2. Importing tracks in the CeNGEN browser

1. Using CeNGEN tracks in other genome browsers

In the genome browser, we can open the track-specific menu by clicking on the three dots symbol next to the track name (either in the track selector or for a track loaded in the browser).

When we select “About track”, we get additional information, notably a link to the file location.

You can use this link to download the file on your computer. Alternatively, you can right-click and “Copy link”.

UCSC browser

Now, open the UCSC browser, you can scroll down to find the “Add custom tracks” button.

Since the tracks we provide are either bigBed (.bb) or bigWig (.bw), you can directly paste their link in the form and click “Submit”, then on the next page, “Return to current position”.

The new track should appear in the browser, along with other tracks you may have loaded.

You can right-click on the track name to change its display mode (e.g. “pack” might be a more useful view).

Wormbase browser

Similarly, you can open the Wormbase browser and add a track either with “FILE>Open track…” or the big “+” sign in the track selector.

In principle, you can directly paste the URL to the track, but this is currently incompatible, instead download the track on your computer and use the “File” selector to add it to the browser.

2. Importing tracks in the CeNGEN browser

If you have a track, e.g. a bam file from RNA-Seq data, or a track obtained from another genome browser, you can import it through the same procedure as described above for the Wormbase browser.

Note that most tracks are not in bigWig or bigBed format and will need indexing. This can often be done with IGVtools, included in the IGV browser (first download IGV, then you can use the menu Tools>Run igvtools).