Navigating Through the View

A user can browse through the results by using one of the tools in the navigation bar (on the top of the view). Select tracks tool is the topic of a separate section, while the remaining tools are described below.

Search box

The Search box can be used to zoom to genomic features that are available in the annotation track. Start typing a search term and it will show you the first 10 suggestions. To select one, use the arrow keys or mouse, or type the full feature name and hit enter.

Position box

The Position box enables the user to visualize a region in the genome. Coordinates are accepted in the following format: chromosome:start – end (zero-based). To show an entire chromosome, it is sufficient to enter just the chromosome number. The U-turn icon on the right of the position box takes you back to the original view, i.e. resets the zoom level to the view that was shown when the viewer was first opened.

Mode selector

Next, the mode selector helps you to quickly navigate through the results. From the left, there is pointer mode, zoom mode, and pan mode.

When pointer mode is activated, the appearance of the cursor will change to an arrow. Pointer mode provides details on any item (e.g. short sequencing read, variant, microarray probe, annotation feature) selected on the canvas. The selected item is highlighted by a green box.

When zoom mode is activated, the appearance of the cursor will change to a plus sign ( + ). With the zoom mode on, you can magnify a specific region by positioning the cursor ( + ) to the left of the area of interest and then left-click & drag the mouse to the right of the area of interest. When the viewer refreshes, it will come "closer" to the region that was selected (by halving the number of basis displayed on the screen).

Alternatively, left-click on the canvas, it will zoom in one level, by halving the number of bases visible on the screen. To zoom out one level Ctrl & left-click should be used; as a result, the number of visible bases will be roughly doubled.

When pan mode is activated, the appearance of the cursor will change to four arrows. Left-click and drag the canvas to the left or to the right to move upstream or downstream in the genome, respectively.

Zoom slider

Zooming out and in can also be achieved with the zoom tool by moving the slider left or right, respectively, or by clicking the magnifying glass icons (– and +).

Bookmark tool

The Bookmark tool enables you to save the location of an interesting region. After zoom to the location of an interesting region, select the bookmark icon (i.e. the star) opens the dialog. To create a new bookmark, type the name of the region in the Create bookmark box and push Create.

Next time you want to go directly to the same location, click on the name of the bookmark will plot the region as defined in the Location column. To remove a bookmark, click on the bin icon .

Save view

Once the plot has been modified, you can save the current appearance of the canvas by using the save icon . The resulting dialog enables you to change the image Format (options include: .svg, .png, .pdf), Size, and Resolution. The image will be saved into your Downloads directory.