Cell metadata

Publish Cell attributes to a project

Cell level attributes can be used for filtering, cell selection, classification and differential analysis using the Publish Cell attributes to project task. Data nodes in the Analyses pipeline that contain this cell level information (e.g. Graph-based clusters data node) can be published to the project and will then be available in Study > Analysis > Metadata > Manage under Cell attributes where they can be modified and reordered.

Annotate cells

If you have attribute information about your cells, you can use the Annotate cells task in Connected Multiomics to apply this information to the data. Once applied, these can be used like any other attributes, and thus can be used for cell selection, classification and differential analysis.

To run Annotate cells:

• Click a Single cell counts data node

• Click the Annotation/Metadata section in the toolbox

• Click Annotate cells

You will be prompted to specify annotation input options:

• Single file (all samples): requires one .txt file for all cells in all samples. Each row in the file represents a barcode and at least one barcode column which will match the barcodes in your data. It also requires a column containing Sample ID which must match the Sample name in the Metadata tab of your project.

• File per sample: requires the format of all of the annotation files to be the same. Each file has barcodes on rows, it requires one barcode column that will match the barcodes in your data in that sample. All files should have the same set of columns, column headers are case sensitive.