Running the Coverage analysis tool

To run the Coverage analysis tool:

        Toolbox | Resequencing Analysis (Image resequencing) | Coverage Analysis (Image copy_number_variation_16_n_p)

This opens the dialog shown in figure 19.66.

Image coverageanalysis_step2
Figure 19.66: Select read mapping results.

Select a reads track or read mapping and click Next. This opens the dialog shown in figure 19.67.

Image coverageanalysis_step3
Figure 19.67: Specify the p-value cutoff.

Set the p-value and minimum length cutoff.

Click Next and specify the result handling (figure 19.68). Selecting the "Create regions" will generate the annotation track, while selecting the "Create report" will generate the report described above. Both options are pre-selected by default.

Image coverageanalysis_step4
Figure 19.68: Specify the output.

Open or save and click Finish.

An example of a track output of the Coverage analysis tool is shown in figure 19.69.

Image CoverageAnalysisOutput_track
Figure 19.69: An example of a track output of the Coverage analysis tool.

The Coverage Analysis table includes the following columns (figure 19.70):

The name is taken from the reference sequence used for mapping
The start and end position of this region on the reference sequence
The type of annotation: high or low coverage
The calculated significance p-value for this region
The length of the region

Image cnv_table_output
Figure 19.70: The table output with detailed information on each region.

For the visual inspection and comparison to known gene/transcripts or other kind of annotations, all region are also annotated on the read mapping.