In projects with multiple data types for each sample such as CITE-Seq, Merge matrices can be used to combine two data nodes with different data types into one data node. 

Prerequisites for running Merge matrices 

1. There must samples with more than one type of data in the project
2. There must be separate counts data nodes for each data type

Running Merge matrices

• Click the first counts data node
• Click the Pre-analysis tools section of the toolbox
• Click Merge matrices 

A second data node of a different type than the first selected data node is chosen automatically. The second data node can selected manually using the Select data node button. 

• Click Select data node to choose the second data node you want to merge (Figure 1)

• Double-click the second data node to select it (Figure 2)

• Click Finish to run

A Merged counts data node is produced (Figure 3). 

The intersection of observations (cells and/or samples) from the two input matrices is included in the merged matrix. 

Once two data types have been merged, they can be split using Split matrix.

For a practical example using Merge matrices, please see our tutorial on Analyzing CITE-Seq Data,