Support for analysis of data from the following types of QIAseq panels/QIAseq library kits is provided under the QIAseq Sample Analysis folder of the Toolbox:
QIAseq sample analysis
- Targeted DNA for variant calling
- Targeted RNAscan for fusion gene detection
- Targeted RNA for differential expression
- Targeted TMB/MSI for tumor mutational burden and microsatellite stability analyses
- Targeted Methyl for differential methylation
- UPX 3' Transcriptome for differential expression
- UPXome for differential expression
- Multimodal for variant calling and fusion gene detection
- Multimodal TMB/MSI for variant calling and fusion gene detection
- Exome for variant calling and trio analysis
- Immune for T-cell receptor repertoire characterization
- RNA Fusion XP for fusion detection, variant calling and differential expression
In addition to template workflows, which can be launched directly, we provide the Analyze QIAseq Samples guide, from where these workflows, calibrated for optimal performance on data generated by the corresponding QIAseq panel, can be launched.
As the Analyze QIAseq Samples guide simplifies most steps necessary when running a QIAseq workflow, it is particularly suitable for first-time users. All application-specific workflows in the Template Workflows section from the toolbox can be used to make copies of the workflow with different configuration settings, a feature useful when working with QIAseq custom panels. In addition, all independent tools that were used to build the template workflows are available in the Biomedical Genomics Analysis folder in the toolbox.
As the workflows are build to fit the different kits and QIAseq protocols the template workflows are made for these specific designs. We recommend performing a QC assessment of the read structure before launching the sample in the Analyze QIAseq Samples guide or the standalone workflows using Validate QIAseq Read Structure (beta).
- The Analyze QIAseq Samples guide
- How to create a custom sample analysis workflow
- Create a custom Trim adapter list (optional)