Annotate cells

If you have attribute information about your cells, you can use the Annotate cells task in Partek Flow to apply this information to the data. Once applied, these can be used like any other attribute in Partek Flow, 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.

Browse to each sample file on the Partek Flow server to specify annotation files for all of the samples in the dialog (Figure 1).

Figure 1. Selecting a cell annotation file

To view a preview of the file, click Show Preview (Figure 2).

Figure 2. Annotation files should have cells on rows and cell attributes on columns

If you would like to annotate your matrix features with a gene annotation file, you can choose an annotation file at the bottom on the dialog. You can choose any gene/feature annotation available on the Partek Flow server. If a feature annotation is selected, the percentage of mitochondrial reads will be calculated using the selected annotation file.

• Click Next to continue

The next dialog page previews the attributes found in the annotations text file (Figure 3).

Figure 3. Previewing attributes to import

You can choose which attributes to import using the check-boxes, change the names of attributes using the text fields, and indicate whether an attribute with numbers is categorical or numeric.

• Click Finish to import the attributes

A new data node, Annotated single cell counts, will be generated (Figure 4).

Figure 4. Output of annotate cells

You annotations will be available in downstream analysis tasks.

Additional Assistance

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