3 Exercises

3.1 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.

Questions

Check the data report and answer the questions.

How many cells were recovered?
Answer
- 1,195 nuclei were recovered.
Which version of Cell Ranger ATAC is used?
Answer
- Single Cell ATAC dataset analyzed using Cell Ranger ATAC 1.1.0
What version of the genome did they use?
Answer
- hg19

Pre-processing workflow

flowchart LR    
  A(Import Data) --> B(Annotation)     
  B --> C(Computing QC metrics)     
  C --> D(Normalization and linear \ndimensional reduction)      
  D --> E(Non-linear dimensional \nreduction and clustering)

Exercise in Google Colab

Create a copy of the Google colab notebook part 13 on your one drive.
Run the exercise.

3.2 References

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