Configure tracks and track display settings

This tutorial demonstrates how to manage tracks in the Graphical Sequence View (GSV). After completing it, you will know how to hide/add tracks, adjust track display settings and change parameters available to some track types.

Genome Workbench offers a list of different tracks such as sequence tracks (e.g. scaffolds, tiling path tracks, etc.), feature tracks (e.g. gene tracks, intron feature, biological regions tracks, etc.), alignment tracks (e.g. alternate loci alignments, RefSeq alignments, pseudogene/paralogous alignments. etc.) and graph tracks (e.g. exon coverage, intron spanning, different expression experiments, epigenomics data, etc.).

Available tracks are different for different organisms. For this tutorial we will use the human chromosome NC_000019. Perform: File => Open => Data from GenBank (NC_000019) => Next => Create New Project => Finish and open this chromosome in the Genome Sequence View. If you didn’t change the default setting previously, you should see the default set of tracks for this chromosome. If you customized the graphical sequence view, Genome Workbench will remember your settings and open your custom configuration the next time you open the same organism/molecule.

Track configure menu and track context menus

To add/hide tracks in the graphical view you can use:

• Configure Tracks dialog (gear icon on upper panel).
• General content menu (point mouse cursor to the black triangle icon at the bottom of the graphical view).
• Content menu for group of tracks belonging to the same category (hover over the category track header to reveal options and select the black triangle icon at the right corner of the header line).

Fig.1 Where to find Configure track dialog and Context menus.

The Configure Tracks dialog (Fig.2) allows you to see a list of the Visible Tracks, All Tracks available, and tracks sorted by the different categories, such as Sequence, Variations, Graphs, etc. (need to select category by clicking on its name in the left part of the dialog). Also, you can search for tracks using the search option in the dialog. To add/hide tracks in the graphical view, just add/remove checkmarks for the tracks of interest and click the OK button.

Fig.2 Configure tracks dialog.

You may prefer to use the context menu to manage the set of tracks in the graphical view. The context menu at the bottom of the GSV allows you to add individual tracks (e.g. scaffolds, tiling path, CCDS genes), whole track category (e.g. graphs, alignments), or group of tracks (e.g. SNP, structural variants). The context menu for the track categories or the group of tracks allows you to add individual tracks to the view (see Fig.3). In case the list of the tracks in the context menu is too long, clicking on the “More…” option will open the Configure Tracks dialog.

Fig.3 Context menu for the SNP group of 29 tracks.

To hide a track from the GSV directly, just hover over the track name to reveal options and click on the “X” icon. To collapse/expand tracks, use the “-“/”+” option on the left side of the track header or the ”-“/”+” icon on the right.

Fig.4 Track hide and expend/collapse options in group/GSV.

To change the tracks order in the graphical view, point the mouse cursor to the track name or group/category name and drag to the new location. You can change track order inside of the group/category or change order of groups/categories with all tracks included.

Track display options

To use individual track display options, mouse over the track name. It will highlight the track header and uncover the track display options (Fig.5). Options are different for the different track types (e.g. Genes (feature tracks), Graphs, Alignments):

Fig.5 Track display options icons.

For the Gene track (feature track type) different gene/RNA/protein merge/show/hide combinations are available:

Fig.6 Gene track display options.

For the alignment tracks, display settings that can be adjusted include alignment statistics, score coloration, sorting, feature projection, and unaligned tails show/hide options.

Fig.7 Alignment track display options.

For the graph tracks, the set of graph rendering options are available in a pop-up dialog. To open this dialog just double click on the graph track itself or click on the settings icon and select the accession number in the settings menu.

Fig.8 Graph rendering options.

The dialog allows you to adjust the graph view in terms of the different types of graphs (smear, histogram (default) and line graph), different scale display options (linear (default) or logarithmic), and options for trimming outliers. The latest option could be useful in case there are large outliers in the data values. Clipping these values can make it easier to visualize data of interest.

The image below (Fig.9) represents a customized view for genes, alignment, and graph tracks with following settings different from default:

• for the genes track – hide gene feature bar and merge all RNAs and proteins;
• for the graph track – line graph/linear, graph height is 50, clip outliers is on, and standard deviation clip threshold is 3;
• for the alignment track – show labels, alignment statistics, and project features for aligned sequences.

Fig.9 Customized tracks view.