Perform QIAseq Multimodal RNA Lib Kit Analysis
The Perform QIAseq Multimodal RNA Lib Kit Expression Analysis (Illumina) and the Perform QIAseq Multimodal RNA Lib Kit Expression Analysis and Fusion Calling (Illumina) workflows can be used for analyzing RNA data produced with the QIAseq Multimodal DNA/RNA Lib Kit.
The workflows include all necessary steps for processing and analyzing the RNA reads:
- Various statistics summarizing and visualizing the input RNA reads are produced using QC for Sequencing Reads, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Sequencing_Reads.html
- UMIs are removed using Remove and Annotate with Unique Molecular Index
- Reads are trimmed using Trim Reads, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_Reads.html
- UMI reads are created using Create UMI Reads from Reads
- Expression is quantified using RNA-Seq Analysis, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_Analysis.html
- Fusions are detected using Detect and Refine Fusion Genes, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Detect_Refine_Fusion_Genes.html
- A summary report is created using Create Sample Report, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html
Fusion detection is only performed in the Perform QIAseq Multimodal RNA Lib Kit Expression Analysis and Fusion Calling (Illumina) workflow. 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
Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
)
and select:
Perform QIAseq Multimodal RNA Lib Kit Expression Analysis (Illumina) (
)
Perform QIAseq Multimodal RNA Lib Kit Expression Analysis and Fusion Calling (Illumina) ()
For general information about launching workflows, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Launching_workflows_individually_in_batches.html
Options can be configured in the following dialogs:
- 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.
- Select Reads. Select the RNA reads. When analyzing more than one sample at a time, check the Batch checkbox in the lower left corner of the dialog.
- Select reference data set. Select the QIAseq Multimodal Library Kit and Hybrid Capture hg38 Reference Data Set, see Reference data management for details.
- Configure batching. If running the workflow in Batch mode, you will be asked to define the batch units. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html for details.
- Detect and Refine Fusion Genes.
Check or uncheck the following options as needed:
- Ignore fusions of overlapping genes on opposite strands
- Detect exon skippings
- Detect with novel exon boundaries
- Allow fusions with novel exon boundaries in both genes
- 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 workflows are also available in the QIAseq Panel Analysis Assistant under Multimodal Library Kit.
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