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It can be interesting to perform exploratory analysis on the two feature types separately. For example, you might be interested to see how the clustering of the same cells differs between protein expression profiles vs. gene expression profiles. To do this

To perform exploratory analysis on the two feature types separately, select the Merged counts data node, click Pre-analysis tools, followed by Split by feature type from the toolbox. A new task, Split by feature type, will be added to the pipeline resulting in two output data nodes: Antibody capture (protein data) and Gene expression (mRNA data). Both contain the same high-quality cells.

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