Perform QIAseq Targeted TCR Analysis

Using RNA-Seq data produced with the QIAseq Targeted RNA Panel TCR Kit, the Perform QIAseq Targeted TCR 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:

To run Perform QIAseq Targeted TCR Analysis, go to the toolbox and select:

        Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | Other QIAseq Workflows (Image qiaseq_workflows_folder_closed_16_n_p) | Perform QIAseq Targeted TCR Analysis (Image immune_rept_wf_16_n_p)

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 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 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.

If only specific chains have been sequenced, set 'Restrict to chains' accordingly in the "Immune Repertoire Analysis" dialog. See Immune Repertoire Analysis for more details.

In the "Filter Immune Repertoire" dialog, clonotypes supported by few UMI reads can be discarded as false positives by ticking 'Use minimum count' and setting the 'Minimum count'. See Filter Immune Repertoire for more details.

Finally, 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 (see QIAseq Panel Analysis Assistant) under Immune.

When launching from the assistant, the analysis can be restricted to the sequenced chains (figure 15.4).

Image select_chain_panel_guide
Figure 15.4: Selecting the chains to be used for the analysis when executing the workflow from the QIAseq Panel Analysis Assistant.