e-learning
Single-cell ATAC-seq standard processing with SnapATAC2
Abstract
Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) analysis is a method to decipher the chromatin states of the analyzed cells. In general, genes are only expressed in accessible (i.e. "open") chromatin and not in closed chromatin.
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- What does ATAC-seq data tell us about the cell?
- Which steps are necessary to cluster the cells of single-cell ATAC-seq data?
- Why is dimension reduction important for the analysis of single-cell data?
Learning Objectives
- Learn how single-cell ATAC-seq data is processed
- Create a count-matrix from a 10X fragment file
- Perform filtering, dimension reduction and clustering on AnnData matrices
- Generate and filter a cell-by-gene matrix
- Identify marker genes for the clusters and annotate the cell types
Licence: Creative Commons Attribution 4.0 International
Keywords: 10x, Single Cell, epigenetics, single-cell
Target audience: Students
Resource type: e-learning
Version: 2
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Pre-processing of 10X Single-Cell ATAC-seq Datasets
Learning objectives:
- Learn how single-cell ATAC-seq data is processed
- Create a count-matrix from a 10X fragment file
- Perform filtering, dimension reduction and clustering on AnnData matrices
- Generate and filter a cell-by-gene matrix
- Identify marker genes for the clusters and annotate the cell types
Date modified: 2024-08-09
Date published: 2024-07-11
Contributors: Björn Grüning, Pavankumar Videm
External resources:
Activity log
