Main Window

Starting window

When starting the program, the main window looks like the following picture:

../../_images/blank.png

The window can be divided into 4 zones:

  • the main menu (1)
  • the tool bar (2 to 6)
  • the track list (7)
  • the track zone (8)

Using the tool bar, you can:

  • read and input genome coordinates (2)
  • navigate along a chromosome (3)
  • zoom the view (4)
  • hide intronic regions (5)
  • search a gene among loaded genome annotations (6)

Visualizing tracks

After you load some datasets using the “Datasets” menu (1) and navigate using buttons (3) and (4), the view looks like this:

../../_images/tracks.png

The genome coordinates are now visible in the zone (2). Note that the coordinates of the mouse appear in the status bar on the bottom-right corner.

The track list now references two tracks in two different categories. Next to each track’s name, buttons let you change the type of graph. For example, the track “gencode-v7” can be displayed either in expanded view or in compact view, or it can be hidden. Buttons next to each category’s name let you change the view for all the tracks of the category. At the bottom of the list, four buttons can be used to add a track, change the settings of the selected track, duplicate the selected track and delete the selected track.

The track zone contains two tracks. The left part of the track shows the track name on a colored background, which correspond to the color in the track list. The first track shows genome annotations. As for most types of graph, you can see more information by pointing an element with your mouse for a few seconds. You can reorder the tracks by dragging them by their colored left part: click on the colored left part of one track and hold down, then move your mouse to move the track and release on the desired position.

Additional frames

The “Window” menu lets you open other frames to display more information.

When the “Items information” frame is opened, additional information are not displayed in tool tips anymore, but they are visible in the frame. Various identifiers link to their description on reference websites (http://www.ensembl.org, http://www.ncbi.nlm.nih.gov, http://vega.sanger.ac.uk). The following screenshot shows an example, when the mouse hovers over an annotation of the Gencode annotation dataset (version 15).

../../_images/info.png

The “Legend” frame shows the link between colors and values for the tracks which use colors as a way to show scores like the FPKM (Fragments Per Kilobase of exon per Million fragments mapped). The legend appears when you point on a track using colors with your mouse.

../../_images/legend.png

Reorganizing the main window

The various frames be undocked or closed using the icons on the top right corner of the list. You can also move the frames to change their order, dock them on the left or the right part of the window, or place them on the top of each other. The “Window” menu lets you choose which frames should be shown.

When the track list is closed, you can still access most of the track configuration options (change type of view, access track settings, etc.) by clicking on a track with the right button of your mouse. You can still re-open the track list and the other frames via the “Window” menu.