Running the "QC for Target Sequencing" tool

The tool is found in the Toolbox:

        Toolbox | Quality Control (Image quality_control_closed_16_n_p) | QC for Target Sequencing (Image targeted_resequencing)

This opens a wizard where you can select mapping results (Image contig)/ (Image multicontig)/ (Image read_track_16_n_p). Clicking Next will take you to the wizard shown in figure 17.1.

Image targeted_step2
Figure 17.1: Specifying the track of target regions.

Click the Browse (Image browse) icon to select an annotation track that defines the targeted regions of your reference genome.

The Report type allows you to select different sets of predefined coverage thresholds to use for reporting (see below). Furthermore, you will be asked to provide a Minimum coverage threshold. This will be used to provide the length of each target region that has at least this coverage.

Finally, you are asked to specify whether you want to Ignore non-specific matches and Ignore broken pairs. When these are applied reads that are non-specifically mapped or belong to broken pairs will be ignored.

Click Next to specify the type of output you want (see figure 17.2).

Image targeted_step3
Figure 17.2: Specifying how the result should be reported.

There are three options:

Click Finish to create the selected reports.