Immune Repertoire and Expression Analysis from Clonotypes and Matrix
The workflow Immune Repertoire and Expression Analysis from Clonotypes and Matrix takes one or more Expression Matrix (
) / (
) and TCR Cell Clonotypes (
) or BCR Cell Clonotypes (
) as input to jointly analyze scRNA-Seq and scV(D)J-Seq data originating from the same sample or samples. The Expression Matrices and Cell Clonotypes are sent on two different paths, for scRNA-Seq and scV(D)J-Seq data, respectively. The scRNA-Seq path follows the same analysis described in Expression Analysis from Matrix, while the scV(D)J-Seq path ensures that clonotypes are filtered accordingly.
The workflow uses the iterate functionality and allows for a combined analysis of multiple samples to produce:
- a single, multi-sample, normalized Expression Matrix () / ();
- a single, multi-sample, filtered TCR Cell Clonotypes () or BCR Cell Clonotypes ();
- a Dimensionality Reduction Plot (
) associated with the automated clusters, predicted cell types, identified clonotypes and additional cell annotations;
- a Heat Map (
), a Dot Plot (
), and a Violin Plot (
) with the predicted cell types as cell groups;
- a Cell Abundance Heat Map () with the automated clusters and predicted cell types as cell groups;
- a Phase Portrait Plot (
) with per gene information on the velocity dynamics;
- a Velocity Genes Scores (
) allowing identification of velocity genes driving the dynamics.
The workflow can be found in the Template Workflows section here:
Single Cell Workflows (
) | From Imported Data (
) | Immune Repertoire and Expression Analysis from Clonotypes and Matrix (
)
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.
Choose either one or more Expression Matrix () / () and TCR Cell Clonotypes () or BCR Cell Clonotypes () or Select files for import and select the formats that are compatible with the selected inputs.
Read more about import options in Importing data.
For the scRNA-Seq path, a number of options are customizable, see Expression Analysis from Matrix. For the scV(D)J-Seq path, only clonotype filtering is customizable, as described in Immune Repertoire Analysis from Reads (10xV(D)J). Adjustments can be made in a workflow copy, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Creating_editing_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).
|
Note: Reference data elements cannot be configured during workflow execution. If other elements than those provided in the default reference data sets are needed, a custom reference data set can be used, see
http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Custom_Sets.html.
When creating custom reference data sets, the chosen gene track needs to match the gene annotations used for training the provided Cell Type Classifier ( |
) (see
The workflow allows the analysis of multiple samples and you can specify metadata during workflow execution. This is converted to cell annotations and can be used for coloring the cells in the Dimensionality Reduction Plot. However, the workflow expects each sample to be present in just one Expression Matrix, and attempting to define batch units containing more than one Expression Matrix will lead to a failure during execution. Similarly, each sample is expected to be present in just one Cell Clonotypes element. For more details on configuring workflow execution with metadata, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html. Make sure to inspect the batch overview to check that the analysis will be performed correctly.
Subsections