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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

Configure License Server connection

If your organization is running a CLC Network License Manager or CLC License Server, you can configure your Workbench to connect to it to get a license for the module.

To configure the Workbench to connect to a CLC Network License Manager or CLC License Server, select the Configure License Server connection option and click on the Next button. A dialog appears, as shown in figure 14.11.

Figure 14.11: Connecting to a CLC Network License Manager or CLC License Server.

The options in that dialog are:

• Enable license server connection. This box must be checked for the Workbench is to contact the CLC Network License Manager or CLC License Server to get a license for the CLC Workbench.
• Automatically detect license server. By checking this option the Workbench will look for a CLC Network License Manager or CLC License Server accessible from the Workbench. Automatic server discovery sends UDP broadcasts from the Workbench on port 6200. Available license servers respond to the broadcast. The Workbench then uses TCP communication for to get a license, if one is available. Automatic server discovery works only on local networks and will not work on WAN or VPN connections. Automatic server discovery is not guaranteed to work on all networks. If you are working on an enterprise network on where local firewalls or routers cut off UDP broadcast traffic, then you may need to configure the details of the CLC Network License Manager or CLC License Server using the Manually specify license server option instead.
• Manually specify license server. Select this option to enter the details of the machine the CLC Network License Manager or CLC License Server software is running on, specifically:
  • Host name. The address of the machine the CLC Network License Manager or CLC License Server software is running on.
  • Port. The port used by the CLC Network License Manager or CLC License Server to receive requests.
• Use custom username when requesting a license. Optional. If this is checked, a username can be entered that will be used when requesting a network license instead of the username of the account being used to run the Workbench.
• Disable license borrowing on this computer. Check this box if you do not want users of the computer to borrow a license for further details.

Special note on modules needing a license

A valid module license is needed to start a module tool, or a workflow including a module tool. Network licenses for modules are valid for four hours after starting the tool or the workflow. A process started (whether a module tool or a workflow including a module tool) will always be completed, even if its completion exceeds the four hours period where the license is valid.

If the tool or the workflow completes before the four hour validity period, it is possible to start a new tool or a workflow, and this will always refresh the validity of the license to a full four hours period. However, if the tool or the workflow completes after the four hour validity period, a new license will need to be requested after that to start the next tool or workflow.

These measures ensure that more licenses are available to active users, rather than blocked on an inactive computer, i.e., where the workbench would be open but not in use.

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Subsections

• Borrowing a license
• Common issues when using a network license

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