Start a QIAseq panel analysis

The Analyze QIAseq Panel Analysis guide offers an easy way to launch ready-to-use workflows optimized for the type of analysis being run. There are several tabs, one for each application category. Under each tab, all relevant QIAseq analysis workflows are listed. For Targeted DNA, TMB and MSI Panels, click on the arrow to the right of a workflow name to select the specific analysis type and reveal the Run button (figure 4.4).

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Figure 4.4: Selecting the relevant panel analysis.

Once you are ready to start a particular workflow, click on the Run button.

If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible. Click Next.

You can then select the sequencing reads that should be analyzed (figure 4.5). The workflow can be run in batch mode by click in the Batch box. If multiple sequence lists are selected and the workflow is launched in batch mode, each sequence list would be treated as a batch unit, that is, each list would be used individually as the input for an independent run of the workflow. If multiple sequence lists are selected and the Batch box is not checked, all the lists would be used together as input for a single run of the workflow.

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Figure 4.5: Select the sequencing reads.

If you have not done so before, you will be prompted to download the appropriate reference data (figure 4.6).

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Figure 4.6: Parameters to configure for Targeted DNA workflows, here set at the default values for somatic variant detection.

The Reference Data Sets relevant to particular applications are:

Note that in the targeted regions files provided in the Reference Data Sets, target regions cover 5 bp on each side of the exon.

Depending on the application, there may be parameters that can be configured. For example, for Targeted DNA panels the parameters are as shown in figure 4.7.

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Figure 4.7: Parameters to configure for Targeted DNA workflows, here set at the default values for somatic variant detection.

In the last dialog, choose where you want to save the outputs of the workflow. A description of the output - including help to perform quality control of your data and interpretation of your results - are given in the following application-specific chapters.