Using RNA-Seq data produced with the QIAseq Immune Repertoire RNA Library Kit, the Perform QIAseq Immune Repertoire Analysis workflow can be used to characterize the T cell receptor (TCR) immune repertoire. The workflow includes all necessary steps for processing the RNA-Seq reads and characterizing the repertoire:
- UMIs are removed using Remove and Annotate with Unique Molecular Index;
- UMI reads are created using Create UMI Reads from Reads;
- Overlapping paired reads are merged using Merge Overlapping Pairs;
- Merged and not merged UMI reads are trimmed using Trim Reads;
- Clonotypes are identified using Immune Repertoire Analysis;
- A summary report is created using Create Sample Report.
To run Perform QIAseq Immune Repertoire Analysis, go to the toolbox and select:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | Other QIAseq Workflows () | Perform QIAseq Immune Repertoire Analysis ()
If you are connected to a CLC Server via your 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 the RNA-Seq reads in the "Select Reads" dialog. When analyzing more than one sample at the time, the Batch checkbox in the lower left corner of the dialog should be checked.
In the "Select reference data set" dialog, you need to specify the relevant Reference Data Set, see Reference data sets for immune workflows for details.
When running the workflow in Batch mode, a dialog will now appear where the batch units should be defined. See http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html for details.
The 'Minimum UMI group size' can be set in the "Create UMI Reads from Reads" dialog. Reads belonging to UMI groups supported by fewer reads than this number will be discarded. See Remove and Annotate with Unique Molecular Index and Create UMI Reads from Reads for information about UMI identification and processing.
Finally, choose where to save the data, and press Finish to start the analysis.
The Perform QIAseq Immune Repertoire Analysis workflow can be launched using the Analyze QIAseq Samples guide from the Immune tab, see QIAseq sample analysis. Use Human Immune Repertoire (IMHS-001Z) or Mouse Immune Repertoire (IMMM-001Z), as appropriate.
When executing from the guide, all options are locked to their default values and no configuration is needed.
- Reference data sets for immune workflows
- Output from the Perform QIAseq Immune Repertoire Analysis workflow