Immune Repertoire Analysis from Reads (10xVDJ)

The workflow Immune Repertoire Analysis from Reads (10xVDJ) takes 10xVDJ reads as input and starts by annotating them with cell barcode and UMI, followed by clonotype identification and filtering. The workflow uses iterate functionality and allows for a combined analysis of multiple samples to produce a single, multi-sample, filtered Cell Clonotypes (Image cell_clonotypes_16_n_p).

The workflow can be found in the toolbox here:

        Workflows (Image sc_workflow_folder_open_16_n_p) | From Reads (Image sc_wf_from_reads_folder_open_16_n_p) | Immune Repertoire Analysis from Reads (10xVDJ) (Image sc_tcr_from_reads_16_n_p)

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.

You can choose either one or more Sequence lists or Select files for import and select FASTQ files for importing.

The workflow is configured for 10x Chromium Single Cell V(D)J reads and only clonotype filtering is customizable. Adjustments can be made in a workflow copy, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Editing_existing_workflows.html.

The workflow can be run using Single Cell hg38 (Ensembl) or Single Cell Mouse (Ensembl) reference data sets (see The Reference Data Manager).

The workflow allows the analysis of multiple samples and you can specify metadata during workflow execution for configuring which inputs belong to which sample. When there is only FASTQ file per sample, metadata is not necessary and "Use organization of input data" can be used. For more details on configuring workflow execution with metadata, see  https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Batching_part_workflow.html. Make sure to inspect the batch overview to check that the analysis will be performed correctly.

Examples for how to use metadata for workflow execution can be found in Configuring the batch units.

The Filter Cell Clonotypes (Image sc_cell_clonotypes_filter_16_n_p) tool in the workflow is configured with most parameters locked, see 11.6. The "Barcodes with multiple clonotypes" option is open, allowing different handling of barcodes with more than on clonotype, see Filter Cell Clonotypes for details. The default option Retain primary retains only the clonotype with the highest number of reads.

Image tcr_filter_settings
Figure 11.6: Workflow settings of the Filter Cell Clonotypes tool.



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