Running the "QC for Read Mapping" tool

The tool is found in the Toolbox:

        Toolbox | Quality Control (Image quality_control_closed_16_n_p) | QC for Read Mapping (Image QC_read_mapping_16_n_p)

This opens a dialog where you can select mapping results (Image contig)/ (Image multicontig)/ (Image read_track_16_n_p) or RNA-Seq analysis results (Image rnaseq).

Clicking Next will display the dialog shown in figure 19.12

Image qc_for_read_mapping_step3
Figure 19.1: Parameters for mapping reports.

The next wizard step shows the used thresholds for the mapping report. These parameters cannot be modified by the user (as thresholds can only be specified for de novo assemblies that does not have a consensus sequence). Whenever a consensus sequence is present the "De novo assembly contig grouping" options are disabled.

Click Next to select output options as shown in figure 19.13

Image qc_for_read_mapping_step4
Figure 19.2: Optionally create a table with detailed statistics per reference.

Per default, an overall report will be created as described below. In addition, by checking Create table with statistics for each mapping, you can create a table showing detailed statistics for each reference sequence. The following sections describe the information produced.