Tracks panel

Tracks are rows of information that can be displayed or hidden, as desired, in the Alignment and Strategy views. Data for some tracks are imported automatically with the sequence data (e.g., feature tracks), while others are calculated with SeqMan Ultra.

The following table shows tasks that affect the display of tracks:

Task	How to…
To display a track	To display a track in the Alignment and/or Strategy views: Open the Tracks panel by clicking on the Tracks tab (). If the tab is not visible, reveal it using Choose View > Tracks > Tracks or View > Reset Panel Layout. The uppermost part of the Tracks panel lets you specify which tracks are visible, and configure their options and appearance. Not all tracks will be available for all projects. For those tracks that are available, some will be displayed and other will be hidden, by default. Put check marks next to available tracks that you wish to display, and remove check marks next to tracks that you wish to hide. Tracks are added to the views in the same order in which their boxes are checked in the Tracks panel. This means that the position of a track may change when its box is unchecked and then checked again. In the Alignment or Strategy view(s) click on the plus sign next to the track name to reveal it.
To expand/collapse selected tracks	Click the plus/minus signs ( / ) to the left of the sequence name. In the Alignment view, you can also right-click on a track and choose Expand or Collapse.
To expand/collapse all tracks in the Alignment view	Right-click anywhere in the Alignment view and choose Expand All or “Collapse All*.
To hide tracks	Do one of the following: To hide a specific track from all views, uncheck the box next to the name of the track in the Tracks panel (see top row of this table). To hide a specific track in one view only, right-click on the track within that view and choose Hide Track. To remove a selected track as if unchecking its box in the Tracks panel, use Edit > Delete or press the Delete key.
To change the order of tracks in a view	Open a sequence row to view its track. Then drag a track label (e.g. “Features”) to the desired position among the other tracks and drop it there. Note that if you turn off some tracks in the Tracks panel and add them again later, they will appear in the order in which their boxes were checked.
To change options for a track	See Edit track options.
To change track height or spacing between tracks	See Change track height or spacing between tracks.
To manually rename a single selected track	Select a track in the Alignment or Strategy view, then right-click on it and choose Rename. Alternatively, select the track name and choose Edit > Rename. The Choose Label dialog opens with the Display drop-down menu set to Custom label. Type the desired name into the Label text box, then click OK.
To automatically rename tracks using specified data fields	Select one or more tracks in the Alignment or Strategy view, then right-click on it and choose Rename with Fields. Alternatively, select the track name and choose Edit > Rename with Fields. Making no selection prior to using the main menu command is equivalent to selecting all tracks. The Choose Label dialog opens with the Display drop-down menu set to One or more fields. The left pane shows available fields, and the right pane shows fields that will be displayed as part of the sequence name. Initially, Default name is the only field listed in the right pane. An example showing the appearance of the name using the specified field(s) appears in the Example box at the bottom of the dialog. Select and organize the fields you wish to display as part of the sequence name: To add or remove items, move them between panes using the left and right arrows ( ). Use the up and down arrows on the right ( ) to specify the order in which displayed fields should appear. By default, a hyphen (-) is included between each of the displayed fields. If desired, type in a different Separator. Or remove all text in the Separator box to include nothing between the fields. The Example text box shows what the label will look like with the current selections. This text can be manually edited, if desired. When you are satisfied with the choices made in this dialog, click OK