Analyze QIAseq UPX 3' RNA
The Analyze QIAseq UPX 3' RNA (Illumina) template workflow can be used for analyzing data produced with a QIAseq UPX 3' Transcriptome Kit or a QIAseq UPX 3' Targeted RNA Panel.
The workflow includes all necessary steps for processing and analyzing reads that have been demultiplexed with Demultiplex QIAseq UPX 3' 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.
- A summary report is created using Create Sample Report.
The workflow always reports expression across the whole genome, which allows you to see when reads map off-target.
Launching the workflow
To run this workflow, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | QIAseq RNA Workflows (
) | Analyze QIAseq UPX 3' RNA (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.
- 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 UPX 3' 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.
- RNA-Seq Analysis.
Specify whether spike-in controls were used when producing the data.
Be aware that the workflow is configured to expect reads that are strand specific. This is because the reaction design ensures that reads from 3' fragments will appear forward-stranded (read 1 mapping sense to the transcript). It is not unusual for 5-10% of reads to be dropped in the workflow for having an unexpected strandedness.
- 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.
- 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 Analyze QIAseq UPX 3' RNA (Illumina) workflow is also available in the QIAseq Panel Analysis Assistant under DNA/RNA Library Kit.
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