9  Exercises

9.1 Dataset overview: 1k Peripheral Blood Mononuclear Cells (PBMCs) from a Healthy Donor

For this tutorial, we will be analyzing a single-cell ATAC-seq dataset of human peripheral blood mononuclear cells (PBMCs) provided by 10x Genomics (Next GEM v1.1). The following files are used in this course, all available through the 10x Genomics website:

• The Raw data: Filtered peak barcode matrix.

• The Metadata: Per-barcode fragment counts & metrics.

• The fragments file: Barcoded and aligned fragment file.

• The fragments file index: Fragments file index.

Exercise in Google Colab

1. Create a copy of the Google colab notebook part 16 on your one drive.
2. Run the exercise.

9.2 References

• Signac tutorial - Analyzing PBMC scATAC-seq (Signac tutorial)
• Signac tutorial - Analyzing PBMC scATAC-seq