Analyze QIAseq Multimodal RNA Library Kit
RNA data produced with the QIAseq Multimodal DNA/RNA Library Kit can be analyzed using the following two template workflows:
- Analyze QIAseq Multimodal RNA Library Kit (Illumina) for whole transcriptome sequencing data.
- Analyze QIAseq Hybrid Capture RNA (Illumina) for data that has been subjected to hybrid capture-based target enrichment with the QIAseq xHYB CGP RNA Panel.
The workflows include all necessary steps for processing and analyzing the reads:
- Various statistics summarizing and visualizing the input reads are produced using QC for Sequencing Reads.
- UMIs are removed using Remove and Annotate with Unique Molecular Index.
- Reads are trimmed using Trim Reads.
- UMI reads are created using Create UMI Reads from Reads.
- Expression is quantified using RNA-Seq Analysis.
- Fusions are optionally detected using Detect and Refine Fusion Genes.
- A summary report is created using Create Sample Report.
- A report is optionally prepared for uploading to QCI Interpret using Prepare QCI Interpret Upload.
The sensitivity of fusion detection is improved when RNA libraries are prepared using hybrid capture with Nextera adapter blockers.
Launching the workflows
To run these workflows, go to
Workflows | Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
)
and select:
Analyze QIAseq Hybrid Capture RNA (Illumina) (
)
Analyze QIAseq Multimodal RNA Library Kit (Illumina) ()
See Launching workflows individually and in batches for general information.
Options can be configured in the following wizard steps:
- Choose where to run. If you are connected to a CLC Server via the CLC 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.
- Specify workflow path. The following paths can be configured:
- Detect fusions. Skipping this may reduce workflow execution time.
- Prepare for QCI Interpret. Prepare a report that can later be uploaded to QCI Interpret or QCI Interpret Translational.
- Select Reads. Select the input reads. When analyzing more than one sample at a time, check Batch in the lower left corner of the dialog.
- Specify reference data handling. Select the QIAseq Multimodal RNA Library Kit and Hybrid Capture hg38 Reference Data Set, see Reference data management for details.
- Configure batching, if running the workflow in batch mode. Define the batch units.
- Batch overview, if running the workflow in batch mode. Verify that the batching is as intended.
- Detect and Refine Fusion Genes, if detecting fusions.
Configure the following options as needed:
- Detect exon skippings
- Detect novel exon boundaries
- Detect novel exon boundaries in both genes
- For the Analyze QIAseq Multimodal RNA Library Kit (Illumina) workflow:
- Gene filter action
- Genes for filtering (tracks)
- Fusion filter action
- Fusions for filtering (tables)
- For the Analyze QIAseq Hybrid Capture RNA (Illumina) workflow:
- Fusion filter action
- Fusion for filtering (tables)
By default, the gene filtering options are set such that the workflow detects only fusions involving the genes targeted by the QIAseq xHYB CGP RNA Panel.
For details about the elements used by default in 'Genes for filtering (tracks)' and 'Fusions for filtering (tables)', see Exclude lists. For general details about fusion detection, see Detect and Refine Fusion Genes.
- Create Sample Report. Select relevant summary items and configure thresholds for quality control. These are included in the quality control section of the sample report. The default values are appropriate for most data sets, but may need to be adjusted.
- Prepare QCI Interpret Upload, if preparing a QCI Interpret report. Specify sample name, subject ID, and project.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
Launching using the QIAseq Panel Analysis Assistant
The two workflows are also available in the QIAseq Panel Analysis Assistant. The Analyze QIAseq Multimodal RNA Library Kit (Illumina) workflow is available under DNA/RNA Library Kit, and the Analyze QIAseq Hybrid Capture RNA (Illumina) workflow is available under xHYB CGP.
Subsections