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• Click a Single cell counts data node
• Click the Pre-analysis tools section in the toolbox
• Click Annotate cells

You will be prompted to pick a text file for each sample you want to annotate. If you are importing annotations for multiple samples, the specify annotation input options:

• Single file (all sample): it requires one .txt file for all your cells in all samples, each row in the file represents a barcode, at least one barcode column which will match the barcodes in your data. It also requires an column contains sample ID which will match the sample name in the data tab of your project.
• File per sample: it requires the format of all of the annotation files

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• to be the same.

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•  Each file has barcodes on rows, it requires one barcode column that will match the barcodes in your data in that sample. All files have to have the same set of column, column headers are case sensitive.

You can pick the file for each sample from the Partek Flow server, you have to specify annotation files for all the samples in the dailog (Figure 1). 

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