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 | Genome Browser (Image genome_viewer_closed_16_n_p) | Graphs | Create Mapping Graph

Select the read mapping as shown in figure 19.21 and click on the button labeled Next.

Image create_mapping_graph_step2
Figure 19.21: 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 19.22.

Image create_mapping_graph_step3
Figure 19.22: 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 19.23. Two of the views have been dragged and dropped to other areas of the View Area to be able to see them in the same window. If you would like to learn more about how to do this, please refer to Arrange views in View Area.

Image create_mapping_graph_outputs
Figure 19.23: Three types of graph tracks are shown.

In this example we generated all possible outputs and chose to open them without saving. You can see that the names of the tabs are marked with an asterisk, which indicates that the graph shown in the view area has not been saved or that changes have been made that must be saved if you want to keep them. Three of the generated outputs have been opened. If you would like to see the outputs in the same view, you can do this by creating a genome browser view. Click on the button labeled Create genome Browser View in the upper right corner of each of the graph tracks shown in the View Area. Combining graph tracks in a genome browser view links the individual tracks together, which makes it much easier to compare the different graph tracks.

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.