Visualizing, zooming and navigating tracks

Side Panel

The Side Panel is shown to the right of a track opened in the View Area (figure 23.3). The settings generally allow users to navigate the track using a specific position on a specific chromosome, to find a particular nucleotide sequence or annotation, and to change the text format.

Image tracksidepanel
Figure 23.3: A CDS track with its Side Panel visible to the right.

In the Navigation section of the Track Side Panel, the upper field gives information about which chromosome is currently shown. The drop-down list can be used to jump to a different chromosome. The Location field displays the start and end positions of the shown region of the chromosome, but can also be used to navigate the track: enter a range or a single location point to get the visualization to zoom in the region of interest. It is also possible to enter the name of a chromosome (MT: or 5:), the name of a gene or transcript (BRCA" or DHFR-001), or even the range on a particular gene or transcript (BRCA2:122-124) Finally, the Overview drop-down menu defines what is shown above the track: cytobands, or cytobands with aggregated data. It can also be hidden all together.

Additional settings specific to the type of track being open can be available. For example, you can change a Reads track layout as explained here: Reads tracks Side Panel settings. Similarly, when working with annotation tracks, the settings Track Layout | Labels controls where labels will be displayed in relation to the annotations (figure 23.4).

Image genomebrowsersidepanel_label
Figure 23.4: The Side Panel for annotation tracks showing the Labels drop down menu. .

Once you have changed the visualization of the track to your liking, it is possible to save the settings as described in View settings for the Side Panel.

Additional tools

In a reads track, a vertical scroll bar will appear to the right of the reads when hovering on them to navigate through high coverage regions.

Specified tracks have buttons that will appear under the track name on the left side of the View Area (highlighted in figure 23.5): these buttons can be used to open the track as a table, or jump to the previous and next element.

Image newactionbuttontracks
Figure 23.5: Hovering on a track will show additional buttons under the track name.


It is possible to zoom in and out in a track using the buttons in the lower right-hand corner of the View Area.

When zooming out you will see that the data is visualized in an aggregated format using a density bar plot or a graph.

Navigation and zooming shortcuts

You can also use the zoom and scroll shortcuts described in the table below:

Action Windows/Linux macOS
Vertical scroll in reads tracks Alt + Scroll wheel Alt + Scroll wheel
Vertical scroll in reads tracks, fast Shift+Alt+Scroll wheel Shift+Alt+Scroll wheel
Vertical zoom in graph tracks Ctrl + Scroll wheel Image command_key_web + Scroll wheel
Zoom Ctrl + Scroll wheel Image command_key_web + Scroll wheel
Zoom In Mode Ctrl + 2 Image command_key_web + 2
Zoom In (without clicking) '+' (plus) '+' (plus)
Zoom Out Mode Ctrl + 3 Image command_key_web + 3
Zoom Out (without clicking) '-' (minus) '-' (minus)
Zoom to base level Ctrl + 0 Image command_key_web + 0
Zoom to fit screen Ctrl + 6 Image command_key_web + 6
Zoom to selection Ctrl + 5 Image command_key_web + 5
Reverse zoom mode press and hold Shift press and hold Shift