QC for Read Mapping

Note that this tool can be used to create a detailed report on a read mapping or a de novo assembly.

To create a detailed mapping report:

        Toolbox | Resequencing Analysis | Quality Control | QC for Read Mapping (Image proteinreport)

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 27.11

Image contig_report_step2
Figure 27.11: Parameters for mapping reports.

In the next wizard window "Set contig group", you can set thresholds for grouping long and short contigs. The grouping is used to show statistics like number of contigs, mean length etc. for the contigs in each group. Thresholds can only be specified for de novo assemblies that do not have a consensus sequence, i.e., these options are disabled whenever a consensus sequence is present or if you are working with a read mapping. Note that the de novo assembly in the CLC Genomics Workbench per default only reports contigs longer than 200 bp (this can be changed when running the assembly).

Click Next to select output options as shown in figure 27.12

Image contig_report_step3
Figure 27.12: Result handling options.

By checking "Create table with statistics for each mapping", you can create a table showing detailed statistics for each reference sequence (for de novo results the contigs act as reference sequences, so it will be one row per contig).

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.