It’s time to apply your skills! You’ll now analyse some clean data from the 10X Chromium platform.

Time estimation: 9 hours

Learning objectives:

• Demultiplex single-cell FASTQ data from 10X Genomics
• Learn about transparent matrix formats
• Understand the importance of high and low quality cells
• Describe an AnnData object to store single-cell data
• Explain the preprocessing steps for single-cell data
• Evaluate quality of single-cell data and apply steps to select and filter cells and genes based on QC
• Execute data normalization and scaling
• Identify highly variable genes
• Construct and run a dimensionality reduction using Principal Component Analysis
• Perform a graph-based clustering for cells
• Identify marker genes for the clusters
• Construct and run a cell type annotation for the clusters