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To add transgenes (including gfp or related) to the references files, choose an assembly, create the transgene reference, and merge the references together (e.g. combine mm10 with dttomato). This is the same process for the annotation file.

How do I classify

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cells?

Classification in Partek Flow can be performed manually or with automatic cell classification which is explained in more detail here. Users often want to classify cells by gene expression threshold(s), for details on classification by marker expression click here. Automatic classification needs to be performed on a non-normalized single cell data node; once complete, publish cell attributes to project then use this classification in visualizations and tasks. You may choose to perform Graph-based clustering and K-means clustering to help identify biomarkers that can then be used to identify the clusters and we also provide hosted lists for different cell types. 

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