Setting the sample name

The `annotated reads' are annotated with the sample name (see Interpreting the output of Annotate Single Cell Reads). When jointly analyzing scATAC-Seq or scV(D)J-Seq with matched scRNA-Seq data, it is important that reads originating from the same sample are annotated with the same sample name. This can be configured using the `Sample name' option.

When the tool is run from the Toolbox, the option supports the placeholder {nameOrBatchId}, which sets the sample name to the name of the input. When the tool is run as part of a workflow, this option will set the sample name to the name of the input for simple workflows, and to the name of the batch identifier for batching/iterating workflows.

Note that it can also be set to an explicit name, such as `Individual_1', or to a complex pattern such as `Individual_{nameOrBatchId}_1'.

Additional placeholders are available when the tool is run as part of a workflow (figure 6.4).

Image sample_name
Figure 6.4: Options for configuring the `Sample name' when Annotate Single Cell Reads is run in a workflow.