Analyze QIAseq Targeted TCR
The Analyze QIAseq Targeted TCR (Illumina) template workflow can be used to characterize the T cell receptor (TCR) immune repertoire for RNA-Seq data produced with the QIAseq Targeted RNA-seq Panel for T-cell Receptor.
The workflow includes all necessary steps for processing and analyzing the reads:
- UMIs are removed using Remove and Annotate with Unique Molecular Index.
- Common sequence is removed using Trim Reads.
- UMI reads are created using Create UMI Reads from Reads.
- Overlapping paired UMI reads are merged using Merge Overlapping Pairs.
- Both merged and not merged UMI reads are trimmed using Trim Reads.
- Clonotypes are identified using Immune Repertoire Analysis.
- Identified clonotypes are merged using Merge Immune Repertoire.
- Merged clonotypes are filtered to remove false positives using Filter Immune Repertoire.
- A summary report is created using Create Sample Report.
Launching the workflow
To run this workflow, go to:
Workflows | Template Workflows | Biomedical Workflows (
) | QIAseq Sample Analysis (
) | Other QIAseq Workflows (
) | Analyze QIAseq Targeted TCR (Illumina) (
)
See Launching workflows individually and in batches for general information.
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 Batch in the lower left corner of the dialog.
- Specify reference data handling.
Select the relevant Reference Data Set. The Reference Data Manager (see Reference Data Management) offers two QIAGEN sets:
- QIAseq Immune Repertoire Analysis for analysis of TCR human data.
- QIAseq Immune Repertoire Analysis Mouse for analysis of TCR mouse data.
- 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.
- Create UMI Reads from Reads. Adjust Minimum UMI group size if needed. UMI groups supported by fewer reads than this number will be discarded. See Create UMI Reads from Reads for details.
- Filter Immune Repertoire Reference. Set restrictions for chain and segment type if only specific chains have been sequenced.
- Filter Immune Repertoire. Uncheck Use minimum count if the identified clonotypes should not be filtered. Otherwise, adjust Minimum count if needed. Clonotypes supported by fewer UMI reads than this number will be discarded. See Filter Immune Repertoire for details.
- 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 workflow is also available in the QIAseq Panel Analysis Assistant under Immune.
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