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• Introduction
  • The concept of CLC Single Cell Analysis Module
  • Contact information
  • System requirements and installation
    • System requirements
    • Installation of modules
    • Uninstalling modules
  • Licensing modules
    • Server License
  • The QIAGEN Cell Ontology
  • Reference data management
    • The Reference Data Manager
  • Running tools and workflows
• Data import
  • Import Expression Matrix
  • Import Cell Annotations
  • Import Cell Clusters
  • Import Cell Clonotypes
• Data export
  • Export Cell Ranger HDF5 expression matrix
  • Export Loom expression matrix
  • Export MEX expression matrix
• Creating a count matrix from FASTQ
  • Annotate Reads with Cell and UMI
    • Setting the sample name
    • Interpreting the output of Annotate Reads with Cell and UMI
  • Single Cell RNA-Seq Analysis
    • The Single Cell RNA-Seq Analysis report
    • The Single Cell RNA-Seq Analysis algorithm
• Cell preparation
  • 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
  • Combine Cell Annotations
  • Combine Cell Clusters
  • Convert Metadata to Cell Annotations
  • Update to Common Sample Name
• Noise reduction through feature selection and PCA
  • Feature selection and PCA
    • Calculation of estimated biological variation
• Cell Annotation
  • Predict Cell Types
  • Train Cell Type Classifier
    • Features used for training and prediction
    • Interpreting the output of Train Cell Type Classifier
    • SVMs for cell type classification
  • 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
• Dimensionality reduction
  • Create UMAP Plot
  • Create tSNE Plot
  • Add Information to Plot
• 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
• Immune Repertoire
  • Single Cell Immune Repertoire Analysis
    • The report output from Single Cell Immune Repertoire Analysis
    • The Cell Clonotypes element
    • The clonotype identification algorithm
  • Filter Cell Clonotypes
  • Combine Cell Clonotypes
  • Compare Single Cell Immune Repertoires
    • Interpreting the output of Compare Single Cell Immune Repertoires
  • Convert Clonotypes to Cell Annotations
• Single cell workflows from reads
  • Expression Analysis from Reads
    • Configuring the batch units
    • Output from Expression Analysis from Reads
  • Immune Repertoire Analysis from Reads (10xVDJ)
    • Output from Immune Repertoire Analysis from Reads (10xVDJ)
  • Immune Repertoire and Expression Analysis from Reads (10xVDJ)
    • Configuring the batch units with multiple input types
    • Output from Immune Repertoire and Expression Analysis from Reads (10xVDJ)
• Single cell workflows from imported data
  • Expression Analysis from Matrix
    • Output from Expression Analysis from Matrix
  • Immune Repertoire and Expression Analysis from Clonotypes and Matrix
    • Output from Immune Repertoire and Expression Analysis from Clonotypes and Matrix
• UMAP and tSNE plot functionality
  • Manual Annotation
  • Create Subset
  • Extract to Table
  • Launching of Create Expression Plot
  • Launching of Create Heat Map for Cell Abundance
  • Launching of Differential Expression for Single Cell
• Licensing requirements for the CLC Single Cell Analysis Module
  • Licensing modules on a Workbench
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure License Server connection
    • Download a static license on a non-networked computer
  • Licensing Server Extensions on a CLC Server
    • Download a static license on a non-networked machine
• Bibliography

Import Cell Clonotypes

The following cell clonotypes formats produced by Cell Ranger can be imported into a Cell Clonotypes () element:

• Import Cell Clonotypes in Cell Ranger Contig Format (): CSV contig format;
• Import Cell Clonotypes in AIRR Format (): AIRR format.

The importers can be found here:

        Import () | Import Cell Clonotypes ()

Most options are common to both importers. The following options can be adjusted (figure 2.6):

Figure 2.6: Options in the dialog of Import Cell Clonotypes in Cell Ranger Contig Format. The same options are present in the dialog of Import Cell Clonotypes in AIRR Format, where "Contig annotations" is named "AIRR rearrangements".

• Contig annotations / AIRR rearrangements. The input .csv or .tsv file, respectively, following the official Cell Ranger format.
• Reference segments (Optional). A reference data element downloaded from the Reference Data Manager (see The Reference Data Manager) containing the corresponding QIAGEN V and J genes. When supplied, the gene names in the input file will be mapped to those used in the provided element. This is important when comparing imported Cell Clonotypes with those produced by the CLC Single Cell Analysis Module, see Compare Single Cell Immune Repertoires.
• Cell format. How to extract the barcode, and optionally the sample name, from the column containing the barcode. For example:
  • If the cell format is set to "{barcode}-1", then "AAGCT-1" will be interpreted as describing a cell with barcode "AAGCT".
  • If the cell format is set to "{sample}-{barcode}", then "demo-AAGCT" will be interpreted as describing a cell from sample "demo" with barcode "AAGCT".
• Sample (Optional). Sets a custom sample name.
• Expression matrix (Optional). The sample name will be obtained from the supplied Expression Matrix. The importer does not check that the barcodes present in the input file match those in the matrix. If the Expression Matrix contains multiple samples, the importer will fail with a relevant message.

  If none of the above three options provides a sample name, the importer sets it to the name of the input file.

  The importer does not allow setting the sample name using more than one of these three options.

  It is important to set an appropriate sample name when matched scRNA-seq data is available, see Convert Clonotypes to Cell Annotations.

• Only include cells. When this is enabled, barcodes that were not called as cells are not imported.

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