...

To modify the points on the image to show more of the histology use the Style configuration option (Figure 9). 

• Click Style in the left panel
• Move the Opacity slider to the left
• Change the Point size to 3 

...

To save the Data Viewer session, click Save in the left panel and give the session an appropriate name. 

Performing Analysis tasks 

• Click on the title of the project (Colon Cancer) to go back to the Analyses tab (Figure 10)
• Click on the Single cell counts node 

A context-sensitive menu will appear on the right-hand side of the pipeline (Figure 9). This menu toolbox includes tasks that can be performed on the selected counts data node. 

An important step in analyzing single cell RNA-Seq data is to filter out low-quality cells. A few examples of low-quality cells are doublets, cells damaged during cell isolation, or cells with too few counts to be analyzed. Click here for more information on Single cell QA/QC. We will not perform Single cell QA/QC in this tutorial. 

• Click the Filtering drop-down in the toolbox
• Click the Filter Features task 
• Choose Noise reduction
• Exclude features where value <= 0.0 in at least 99.0% of the cells (Figure 11) 
• Click Finish

A task node, Single cell QA/QCFiltered counts node, is produced. Initially, the node will be semi-transparent to indicate that it has been queued, but not completed. A progress bar will appear on the Single cell QA/QC task node to indicate that the task is running.

The plots are highly customizable and can be used to explore the quality of cells in different samples. For more information on navigating Single cell QA/QC 

• Click on Single cell counts in the Get Data icon on the left (Figure 9)
• Click and drag the Sample name attribute onto the Counts plot and drop it onto the X-axis 
• Repeat this for the Detected genes plot

The cells are now separated into different samples along the x-axis (Figure 10)

• Hold Control and left-click to select both plots
• Open the Style icon on the left under Configure
• Under Color, use the slider to reduce the Opacity
• Open the Axis icon on the left
• Adjust the X-rotation on the plots to 90

Note how both plots were modified at the same time. 

Cells can be selected by setting thresholds using the Select & Filter tool. Here, we will select cells based on the total count

...