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

Select the read mapping as shown in figure 23.29 and click on the button labeled Next.

Image create_mapping_graph_step2
Figure 23.29: Creating graph track from mappings.

Select the graph tracks that you would like to create.

One graph track output will be created for each of the graph tracks you have chosen by checking the boxes shown in figure 23.30.

Image create_mapping_graph_step3
Figure 23.30: Choose the types of graph tracks you would like to generate.

The following options exist:

Click on the button labeled 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 23.31.

Image create_mapping_graph_outputs
Figure 23.31: 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 23.34). 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 23.32).

Image zoomedingraph_outputs
Figure 23.32: A graph track zoomed in.