Analyze QIAseq RNA
The Analyze QIAseq RNA (Illumina) template workflow can be used for analyzing data produced with the QIAseq Targeted RNA Panels.
The workflow includes the following steps for processing and analyzing the reads:
- Reads are trimmed using Trim Reads.
- Expression is quantified using Quantify QIAseq RNA.
- A summary report is created using Create Sample Report.
Before running the workflow, make sure proper adapter trimming is performed. Run QC for Sequencing Reads to assess the reads and remove any unexpected adapters before running the workflow. Reads with adapters are likely not to map to the reference which can lead to loss of read count.
Launching the workflow
To run this workflow, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
) | Analyze QIAseq RNA (Illumina) (
)
The workflow can and should be run in batch mode, allowing the analysis of several samples at once. When working in batch mode, it is important to select the folder containing the samples, and not the subfolders containing the sequence lists, nor the reads themselves. In the two latter cases, each sequence list would be considered as an independent sample, when in fact, individual samples are usually made of several sequence lists.
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.
- 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 RNA Panels 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.
- Target regions. Choose the relevant target regions from the drop down list. If the data was produced using a panel that is not available in the list, see QIAseq custom panels.
- 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 workflow is also available in the QIAseq Panel Analysis Assistant under Targeted RNA.
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