Create Mapping Graph

The Create Mapping Graph tool can create a range of different graphs from a read mapping track. To run the tool go to the toolbox:

        Toolbox | Track Tools (Image track_tools) | Graphs (Image graphs_closed_16_h_p) | Create Mapping Graph (Image graph_track_16_n_p)

Select the read mapping as shown in figure 24.30 and click on the button labeled Next.

Image create_mapping_graph_step2
Figure 24.30: Mapping graph tracks containing different types of information can be created.

Select the graph track types to create, as shown in figure 24.31. One graph track is created for each type selected.

Image create_mapping_graph_step3
Figure 24.31: Choose the types of graph tracks to be created.

Each position in a graph track contains the values of the track type selected. These are:

Click Next, choose where to save the generated output(s) and click on the button labeled Finish.

An example of three different outputs is shown in figure 24.32.

Image create_mapping_graph_outputs
Figure 24.32: Three types of graph tracks are shown.

Note that the option "Fix graph bounds" found under Track layout in the Side Panel is useful to manually adjust the numbers on the y-axis.

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 24.35). When zoomed in all the way down to base resolution only one curve will be shown reflecting the exact observation at each individual position (figure 24.33).

Image zoomedingraph_outputs
Figure 24.33: A graph track zoomed in.