Update to Common Sample Name
When jointly analyzing scV(D)J-Seq or scATAC-Seq with matched scRNA-Seq, data originating from the same sample must be annotated with the same sample name. Ideally, this should be done as a first step in the analysis pipeline, when running the Annotate Reads with Cell and UMI tool (see Annotate Reads with Cell and UMI) or when importing the data. If this has not been done, the sample name can be updated using the Update to Common Sample Name tool. It can be found in the Toolbox here:
Utility Tools (
) | Update to Common Sample Name (
)
The tool takes one element as input, of one of the following types:
- Sequence List (
) that has been annotated with the Annotate Reads with Cell and UMI;
- Expression Matrix (
);
- Expression Matrix with spliced and unspliced counts (
);
- Peak Count Matrix (
);
- Velocity Matrix (
);
- Cell Clusters (
);
- Cell Annotations (
);
- TCR Cell Clonotypes (
);
- BCR Cell Clonotypes (
).
A second element is provided in the `Take sample name from' option. The following types are allowed:
- Expression Matrix ();
- Expression Matrix with spliced and unspliced counts ();
- Peak Count Matrix ();
- Velocity Matrix ();
- Cell Clusters ();
- Cell Annotations ();
- TCR Cell Clonotypes ();
- BCR Cell Clonotypes ();
- Dot Plot (
);
- Violin Plot (
);
- Dimensionality Reduction Plot (
).
The tool outputs a copy of the input, where the sample is updated to match that found in the `Take sample name from' element.
Both the input and `Take sample name from' element are required to only contain one sample, as otherwise the sample name cannot be uniquely identified.