Creating graph tracks

Graph tracks can be created from sequences and mappings using the tools in the Toolbox:

        Toolbox | Track Tools (Image track_tools) | Graphs

Graph tracks can also be created directly from the track view or track list view by right-clicking the track you wish to use as input, which will give access to the toolbox.

The Create GC Contents Graph Track tool needs a sequence track as input and will create a graph track with the GC contents of that sequence. This track can then be displayed together with the sequence and other tracks in a track list.

The Create Mapping Graph Tracks can create the following graphs from a mapping track (see figure 24.24).

Image createmappinggraphtracks_step2
Figure 24.1: Creating graph track from mappings.

The Identify Graph Threshold Areas tool uses graph tracks as input to identify graph regions that fall within certain limits (thresholds). The lower and upper thresholds are to be specified by the user (figure 24.25). In cases where a mapping graph track has been used as input, the range for the lower and upper thresholds will depend on the type of graph that was created from the mapping track as well as on the data (coverage, quality etc.).

Image identify_graph_threshold_areas
Figure 24.2: Specification of lower and upper thresholds.

When zoomed out, the graph tracks are composed of three curves showing the maximum, mean, and minimum value observed in a given region (see figure 24.26). When zoomed in only one curve will be shown reflecting the exact observation at each individual position.

Image graph_tracks_three_curves
Figure 24.3: Graph track showing the minimum, mean, and maximum observed values. At the highlighted position the minimum value is 8, the mean value 20 and the maximum value 36.