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 20.11

Image qc_for_read_mapping_step3
Figure 20.1: 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 do not have a consensus sequence).

Click Next to select output options as shown in figure 20.12

Image qc_for_read_mapping_step4
Figure 20.2: Result handling options.

By checking "Create table with statistics for each mapping", you can create a table showing detailed statistics for each reference sequence.

The first section of the detailed report is a summary of the statistics: reference count, type, total reference length, GC contents in %, total read count, mean read length, and total read length

The rest of the report, as well as the optional statistic tables are described in the following sections.