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• Introduction
  • The concept of CLC Single Cell Analysis Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Reference data management
  • QIAGEN Sets
• Running tools and workflows
• Data import
  • Import Cell Annotations
  • Import Cell Clusters
  • Import Cell Clonotypes
  • Import Expression Matrix
    • HDF5 formats
    • Other formats
  • Import Peak Count Matrix
  • Import Space Ranger
  • Cell format in importers
  • Import Immune Reference Segments
    • IMSEQ
    • IMGT
    • Output from Import Immune Reference Segments
• Data export
  • Export Cell Ranger HDF5 Expression Matrix
  • Export AnnData Expression Matrix
  • Export h5Seurat Expression Matrix
  • Export Loom Expression Matrix
  • Export MEX Expression Matrix
  • Export TXT Expression Matrix
  • Export Peak Count Matrix
• Prepare Reads
  • Annotate Single Cell Reads
    • Setting the sample name
    • Interpreting the output of Annotate Single Cell Reads
• Creating a Gene Expression Matrix
  • Single Cell RNA-Seq Analysis
    • The Single Cell RNA-Seq Analysis report
    • The Single Cell RNA-Seq Analysis algorithm
  • QC for Single Cell
    • Empty droplets filter
    • Count-based and extra-chromosomal filters
    • Doublets filter
    • Interpreting the output of QC for Single Cell
    • Choosing barcodes to retain
    • The cell calling algorithm
    • The doublet calling algorithm
  • Normalize Single Cell Data
    • When is batch correction appropriate?
    • Interpreting the output of Normalize Single Cell Data
    • The Normalize Single Cell Data algorithm
• Cell Type Classification
  • Browse QIAGEN Cell Ontology
  • Predict Cell Types
    • Interpreting the output of Predict Cell Types
    • Cell type refinement
  • Train Cell Type Classifier
    • Features used for training and prediction
    • Interpreting the output of Train Cell Type Classifier
    • SVMs for cell type classification
  • Update Cell Type Classifier
  • The Cell Type Classifier element
• Expression Analysis
  • Differential Expression for Single Cell
    • Interpreting the output of Differential Expression for Single Cell
    • The differential expression algorithm
  • Create Expression Plot
    • The Heat Map output of Create Expression Plot
    • The Dot Plot output of Create Expression Plot
    • The Violin Plot output of Create Expression Plot
• Velocity Analysis
  • Single Cell Velocity Analysis
    • Interpreting the output of Single Cell Velocity Analysis
    • The velocity estimation algorithm
  • Differential Velocity for Single Cell
  • Score Velocity Genes
    • Interpreting the output of Score Velocity Genes
  • Create Phase Portrait Plot
  • Velocity analysis in workflows
• Spatial Transcriptomics
  • The Spatial Transcriptomics Plot element
• Chromatin Accessibility
  • Single Cell ATAC-Seq Analysis
    • Interpreting the output of Single Cell ATAC-Seq Analysis
    • The report output from Single Cell ATAC-Seq Analysis
    • The Single Cell ATAC-Seq Analysis algorithm
  • Split Read Mapping by Cell
  • Differential Accessibility for Single Cell
    • The differential accessibility algorithm
• Immune Repertoire
  • Single Cell V(D)J-Seq Analysis
    • The report output from Single Cell V(D)J-Seq Analysis
    • The clonotype identification algorithm
  • The Cell Clonotypes element
    • Primary and secondary clonotypes
    • Cell Clonotypes tables
    • Cell Clonotypes alignments
    • Cell Clonotypes Sankey plot
  • Filter Cell Clonotypes
  • Combine Cell Clonotypes
  • Compare Cell Clonotypes
    • Interpreting the output of Compare Cell Clonotypes
  • Convert Clonotypes to Cell Annotations
• Noise reduction through feature selection and dimensionality reduction
  • Feature selection and dimensionality reduction
    • Calculation of estimated biological variation
• Cell Annotation
  • Cluster Single Cell Data
    • The Cluster Single Cell Data algorithm
  • Create Heat Map for Cell Abundance
    • Interpreting the output of Create Heat Map for Cell Abundance
  • Create Cell Annotations from Hashtags
• Dimensionality reduction
  • UMAP for Single Cell
  • tSNE for Single Cell
• Single cell low-dimensional plots functionality
  • Manual annotation
  • Visualizing different types of matrices
  • Create Subset
  • Extract to Table
  • Launching of Create Expression Plot
  • Launching of Create Heat Map for Cell Abundance
  • Launching of Differential Accessibility for Single Cell
  • Launching of Differential Expression for Single Cell
  • Launching of Differential Velocity for Single Cell
  • Launching of Score Velocity Genes
• Utility tools
  • Combine Cell Annotations
  • Update Cell Annotations
  • Convert Metadata to Cell Annotations
  • Combine Cell Clusters
  • Update Cell Clusters
  • Add Information to Plot
  • Update Single Cell Sample Name
• Single cell template workflows from reads
  • Expression Analysis from Reads
    • Configuring the batch units for Expression Analysis from Reads
    • Output from Expression Analysis from Reads
  • Chromatin Accessibility Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility Analysis from Reads
    • Output from Chromatin Accessibility Analysis from Reads
  • Chromatin Accessibility and Expression Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility and Expression Analysis from Reads
    • Output from Chromatin Accessibility and Expression Analysis from Reads
    • Importing reads
  • Immune Repertoire Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire Analysis from Reads (10xV(D)J)
  • Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Configuring the batch units for Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
• Single cell template workflows from imported data
  • Expression Analysis from Matrix
    • Output from Expression Analysis from Matrix
  • Chromatin Accessibility and Expression Analysis from Matrix
    • Output of Chromatin Accessibility and Expression Analysis from Matrix
  • Immune Repertoire and Expression Analysis from Clonotypes and Matrix
    • Output from Immune Repertoire and Expression Analysis from Clonotypes and Matrix
  • Importing data
• Bibliography

Filter Cell Clonotypes

Sometimes it can be desirable to restrict TCR Cell Clonotypes () or BCR Cell Clonotypes () to only a specific subset, for example only productive clonotypes, or only barcodes that are present in matched scRNA-Seq data. This can be achieved with the Filter Cell Clonotypes tool. Alternatively, the clonotypes can be filtered to a selection in the Cell Clonotypes tables (Cell Clonotypes tables) by using the option "Create Cell Clonotypes from Selection" from the right-click menu.

The Filter Cell Clonotypes tool can be found in the Toolbox here:

        Toolbox | Single Cell Analysis () | Immune Repertoire () | Filter Cell Clonotypes ()

The tool takes a Cell Clonotypes element as input and produces a filtered element.

The following options can be adjusted (figure 13.11):

Figure 13.11: The options in the dialog of the Filter Cell Clonotypes tool.

• Barcodes to retain. Multiple elements containing cells can be provided, such as Expression Matrices, Cell Clusters and Cell Annotations. From these, a set of valid cells, identified through the sample and barcode, is obtained as the intersection of the cells in the chosen elements. When used, only the clonotypes for the valid cells are retained in the output.
• Productive status to retain. A mixture of `Productive', `Out of frame' and `Premature stop codon' can be chosen and only the clonotypes with the respective productive status will be retained. If left empty, no filter is applied.
• Chains to retain. A mixture of:
  • for TCR Cell Clonotypes: TRA, TRB, TRG and TRD;
  • for BCR Cell Clonotypes: IGH, IGK and IGL;
  can be chosen. Only the clonotypes with the respective chains will be retained. If left empty, no filter is applied.
• Combined chains to retain. A mixture of:
  • for TCR Cell Clonotypes: TRA + TRB and TRG + TRG;
  • for BCR Cell Clonotypes: IGH + IGK and IGH + IGL;
  can be chosen. Only clonotypes that contain all chains in the combination are retained. This can be used for removing barcodes for which not all desired chains have been identified. If left empty, no filter is applied.
• Segment types to retain. A mixture of `V', `D', `J' and `C' can be chosen and only the clonotypes that have identified segments for all respective segment types will be retained. This means that, for example, if `D' is chosen, only chains for which the D segment is used will be retained, and for those chains, only the clonotypes for which the identification of the D segment was successful will be retained. If left empty, no filter is applied.
• Multiple clonotypes. Barcodes can have more than one clonotype associated with them, see Primary and secondary clonotypes. Different types of filters can be chosen:
  • Retain all. No filter is applied and all clonotypes are retained.
  • Retain primary. Only the primary clonotypes are retained.
  • Retain secondary. Only the secondary clonotypes are retained.
  • Retain primary and secondary. Both the primary and the secondary clonotypes are retained.
  • Retain none. Only barcodes containing just primary clonotypes are retained.

The options above can be mixed and matched to obtain the desired output. Note that the filters are applied in the order given above.

For example, assume we want to only use the primary TRB clonotypes with D segments. This can be obtained by setting "Chains to retain" to "TRB", "Segment types to retain" to "D", and "Multiple clonotypes" to "Retain primary". If one barcode A has a primary TRB clonotype without D segments and a secondary TRB clonotype with D segments, the former will be removed first and the second with D segments will become the primary one. Hence, "Retain primary" will have no effect on this barcode. If another barcode has two TRB clonotypes with D segments, "Retain primary" will remove the secondary clonotype.

If the desired behavior is that barcode A should be entirely removed from the output, as its primary TRB clonotype does not have D segments, the tool can be run multiple times such that the filters are applied in a different order. By running the tool with "Multiple clonotypes" set to "Retain primary" first, the barcode will have only the clonotype without D segments. A second execution of the tool with "Segment types to retain" set to "D" will entirely remove the barcode.

The Filter Cell Clonotypes tool can optionally produce a report for each sample found in the input element, summarizing the clonotypes left after filtering. The output report includes the same information as the report produced by the Single Cell V(D)J-Seq Analysis tool, minus the assembly and trimming summaries (see The report output from Single Cell V(D)J-Seq Analysis).

To obtain a report summarizing clonotypes across samples, see Compare Single Cell Immune Repertoires.

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