MPG Primer: Understanding Single Cell ATAC-Seq Data Analysis (2024)

Explore the fundamentals of single-cell ATAC-Seq data analysis in this comprehensive 45-minute Medical and Population Genetics Primer lecture. Delve into key concepts such as ATAC technology, combinatorial index-based approaches, and workflow overviews. Learn about essential quality control measures, including TSS Enrichment Scores and doublet detection. Discover dimensionality reduction techniques, clustering methods, and visualization strategies for interpreting complex datasets. Gain insights into popular tools and downstream analysis techniques used in the field. Presented by Dongwon Lee from Boston Children's Hospital, Harvard Medical School, and the Broad Institute of MIT and Harvard, this lecture provides a solid foundation for understanding and applying single-cell ATAC-Seq analysis in genomics research.

Introduction
What is ATAC
Example
Broadness of the peak
Combinatorial indexbased approach
Workflow overview
Adapter training
Fragment files
Cell QC
TSS Enrichment Score
TSS Enrichment Score Visualization
Metric Distribution
Doublets
Doublet Detection
Feature Cell Count
Dimensionality Reduction
TFIDF
Matrix Factorization
Clustering
Hierarchical clustering
Visualization
downstream analysis
popular tools