Track lists

Tracks based on a compatible reference genome can be viewed in a Track List (Image trackset_16_n_p), allowing for easy visualization and comparative analysis (figure 25.14).

The Create Track List (Image create_tracklist_16_h_p) tool can be launched by going to

        Toolbox | Utility Tools (Image utilities_closed_16_n_p) | Tracks (Image track_tools) | Create Track List (Image create_tracklist_16_h_p)

Alternatively, click on the Create Track List button, visible at the bottom of individual tracks when they are open in the View Area.

Image genomebrowser1
Figure 25.14: A track list with 3 tracks. By zooming into a given location, the details of the read mapping (top track), variants(middle track) and overlapping CDS annotations (bottom track) can be investigated.

Track lists refer to tracks, rather than containing them directly. If a track referred to by a track list cannot be found, this will be indicated by marking it as an "Unresolved track" in the track list.

Clicking on icons at the bottom of a track list provides different views of the data. Of note is the Chromosome Table view (Image track_list_tableview_16_h_p), which provides a summary of the data contained in the tracks referred to by the track list. The table in this view contains one row per chromosome, and one column per track in the track list.

Creating track lists within workflows is described in Track lists as workflow outputs.

Working with tracks in track lists

Tracks can be added to, removed from, and re-ordered within track lists. In addition, individual tracks can be opened in linked views, allowing quick navigation to areas of interest in the genome.

Right-clicking on any of the tracks opens up a context menu with several options (figure 25.15). The options presented vary slightly, depending on the track type.

Image organizetracks
Figure 25.15: Options to handle and organize tracks.

Tracks in the list can be re-ordered by dragging them up and down in the open view.

Image trackfromlist_intableview
Figure 25.16: A linked table view of a track is opened by right-clicking on the track in the track list and then selecting "Open This Track".

Making copies of Track Lists

Track Lists can be copied like any other data element (see Moving and copying elements). If a Track List is copied by itself, then this new copy will refer to the same tracks as the original Track List.

To make a copy of a Track List and the tracks it refers to, and to have the new Track List refer to the new copies of the tracks, copy the Track List and all the tracks in a single copy action. If a Track List and a subset of the tracks it refers to are copied, then references to the copied tracks are updated, while references to the original tracks are maintained for those not copied.