Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
The workflow Immune Repertoire and Expression Analysis from Reads (10xV(D)J) takes reads as input and jointly analyzes scRNA-Seq and scV(D)J-Seq data originating from the same sample. The reads are first annotated with cell barcode and UMI, after which they are sent on two different paths, one for each type of data. The workflow splits the reads according to sample and data type, as given through metadata.
The scRNA-Seq and scV(D)J-Seq paths follow the same analysis described in Expression Analysis from Reads and Immune Repertoire Analysis from Reads (10xV(D)J), respectively.
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 (
) element;
- 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.
- If velocity analysis is enabled during execution:
- a Phase Portrait Plot (
) with per gene information on the velocity dynamics;
- a Velocity Genes Scores (
) element allowing identification of velocity genes driving the dynamics.
- a Phase Portrait Plot (
The workflow can be found here:
Template Workflows | Single Cell Workflows (
) | From Reads (
) | Immune Repertoire and Expression Analysis from Reads (10xV(D)J) (
)
If you are connected to a CLC Server via the CLC 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 data. For the scRNA-Seq path, a number of options are customizable, see Expression Analysis from Reads. For the scV(D)J-Seq path, only clonotype filtering is customizable, see Immune Repertoire Analysis from Reads (10xV(D)J). Adjustments can be made in a workflow copy, see https://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 Reference data management).
|
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
https://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 must specify metadata during execution for configuring which reads belong to which sample and data type, see Configuring the batch units for Immune Repertoire and Expression Analysis from Reads (10xV(D)J).
Subsections
- 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)