Running the duplicate reads removal

The tool is found in the Toolbox:

        Toolbox | Resequencing Analysis (Image resequencing_closed_16_n_p) | Remove Duplicate Mapped Reads (Image remove_duplicates)

This opens a dialog where you can select mapping results in read tracks (Image read_track_16_n_p) format. Clicking Next allows you to set the threshold parameters as displayed in figure 21.37.

Image removemappedduplicatereads-step2
Figure 21.37: Setting the stringency for merging similar reads.

The parameter is explained in detail in Algorithm details and parameters.

Clicking Next will reveal the output options. The main output is a list of the reads that remain after the duplicates have been removed. In addition, you can get the following output:

List of duplicate sequences
These are the sequences that have been removed.
This is a brief summary report with the number of reads that have been removed (see an example in figure 21.38).

Image duplicate-mapped-reads-removal-report
Figure 21.38: Summary statistics on the duplicate mapped reads.