Secondary peak calling

CLC Genomics Workbench is able to detect secondary peaks - a peak within a peak - to help discover heterozygous mutations. Looking at the height of the peak below the top peak, the CLC Genomics Workbench considers all positions in a sequence, and if a peak is higher than the threshold set by the user, it will be "called".

The peak is called by changing the residue to an ambiguity character and by adding an annotation at this position.

To call secondary peaks:

        select sequence(s) | Toolbox in the Menu Bar | Molecular Biology Tools (Image lab_work_support) | Sequencing Data Analysis (Image assemblyfolder)| Call Secondary Peaks (Image secondary_peak_calling)

This opens a dialog where you can alter your choice of sequences.

When the sequences are selected, click Next.

This opens the dialog displayed in figure 18.16.

Image secondarypeakcallingstep2
Figure 18.16: Setting parameters secondary peak calling.

The following parameters can be adjusted in the dialog:

Click Next if you wish to adjust how to handle the results. If not, click Finish. This will start the secondary peak calling. A detailed history entry will be added tothe history specifying all the changes made to the sequence.