Running a QIAseq analysis
After starting an analysis using the Run button, a wizard shows, containing multiple steps:
- Choose where to run. If the CLC Workbench is logged into a CLC Server, the first step is to select where to run the analysis. See Running a tool on a CLC Server for details.
- Acquire reference data. If the reference data required for the analysis has not been downloaded previously, it must be downloaded before proceeding. See Reference data for QIAseq analyses for details.
- Select Input(s). Select the data from the relevant QIAseq panel/kit. Typically, this would be the raw reads, but certain analyses require as input outputs produced by other analyses. Depending on the analysis, there might be multiple steps for selecting the inputs.
Inputs can be selected from the Navigation Area. When the analysis is a workflow using reads as input, these can also be imported on-the-fly, see Configuring input and output elements for details.
- Set parameters. Some analyses require that a few parameters are set (figure 14.107).
Figure 14.107: The "Somatic, Illumina" analysis for the DHS-001Z panel allows adjusting the minimum variant frequency and read coverage. - Result handling. Specify if results should be opened or saved. Depending on the type of the analysis, different options are available:
- For workflows, results can only be saved.
The Preview All Parameters button allows to review all parameters used for the workflow execution. Clicking the button opens a new wizard similar to the Configuration Editor view.
Checking Create workflow result metadata creates a Workflow Result Metadata table, see Workflow Result Metadata tables for details.
- For tools, there might be additional tool specific options.
- For workflows, results can only be saved.
- Save location for new elements. Specify where to save the results when selecting "Save" in the previous wizard step. See Handling results for details.
Batching
Analyses can be run individually or in batches by checking the Batch checkbox on the Select Input(s) wizard step. See Batch processing for details.
When the analysis is a workflow, the batch units in the QIAseq Panel Analysis Assistant are always defined by the organization of input data, see Running workflows in batch mode for details. To define batch units based on metadata, see Configuring QIAseq analyses.