The QIAseq Panels Analysis section of the Biomedical Genomics Analysis plugin covers several different types of applications:
- Targeted DNA for variant calling
- Targeted RNAscan for fusion gene detection
- Targeted Multimodal for variant calling and fusion gene detection
- Targeted TMB/MSI for tumor mutational burden and microsatellite stability analyses
- Targeted RNA for differential expression
- UPX 3' for differential expression
- Targeted Methyl for differential methylation
The plugin includes the Analyze QIAseq Panels guide that facilitates running a QIAseq panel analysis: each secondary analysis workflow listed in the guide has been designed and calibrated for optimal performance on data generated by the corresponding QIAseq panel.
As the Analyze QIAseq Panels guide simplifies most steps necessary when running a QIAseq workflow, it is particularly suitable for first-time users. However, the plugin also offers access to all application-specific workflows in the Ready-to-Use section of the Toolbox. These templates can be used to make copies of the workflow with different configuration settings, a feature useful when working QIAseq custom panels. In addition, all independent tools that were used to build the ready-to-use workflows are available in a folder called QIAseq Panel Expert Tools.
Note that the plugin supports panels where, when using paired reads, the UMI has been placed on Read 2. Using a different design will generate sub-optimal results.
- The Analyze QIAseq Panels guide
- How to create a custom panel analysis workflow
- Create a custom Trim adapter list (optional)