Quantify QIAseq UPX 3'
The Quantify QIAseq UPX 3' 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, see Demultiplex QIAseq UPX 3' reads:
- 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
- A summary report is created using Create Sample Report, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html
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 (
) | Quantify QIAseq UPX 3' (
)
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 input reads. When analyzing more than one sample at a time, check the Batch checkbox 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, 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.
- Batch overview, if running 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 specify thresholds for quality control. Summary items, thresholds, and an indication of whether specified thresholds were met, will be shown in the quality control section of the sample report. The default summary items are appropriate for many data sets, but may need to be adjusted. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html for details.
- 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 Quantify QIAseq UPX 3' workflow is also available in the QIAseq Panel Analysis Assistant under UPX 3' RNA.
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