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 detection investigates any secondary high peaks in the same interval as the already called peaks. The peaks must have a peak shape in order to be considered (i.e. a fading signal from the previous peak will be ignored). Note! The secondary peak caller does not call and annotate secondary peaks that have already been called by the Sanger sequencing machine and denoted with an ambiguity code.

Regions that are trimmed (i.e. covered by trim annotations) are ignored in the analysis (Trimming).

When a secondary peak is called, the residue is change to an ambiguity character to reflect that two bases are possible at this position, and optionally an annotation is added at this position.

To call secondary peaks:

        Toolbox | 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 add the sequences to be analyzed. If you had already selected sequence in the Navigation Area, these will be shown in the 'Selected Elements' box. However you can remove these, or add others, by using the arrows to move sequences between the Navigation Area and Selected Elements boxes.

When the sequences are selected, click Next.

This opens the dialog displayed in figure 17.19.

Image secondarypeakcallingstep2
Figure 17.19: Setting parameters secondary peak calling.

The following parameters can be adjusted in the dialog:

Clicking Next allows you to add annotations. In addition to changing the actual sequence, annotations can be added for each base that has been called. The annotations hold information about the fraction of the max peak height.

Click Finish to start the tool. This will start the secondary peak calling. A detailed history entry will be added tothe history specifying all the changes made to the sequence.