e-learning
Pre-processing of 10X Single-Cell ATAC-seq Datasets
Abstract
Similar to bulk ATAC-Seq, single-cell ATAC-Seq (scATAC-seq) leverages the hyperactive Tn5 Transposase to profile open chromatin regions but at single-cell resolution. Thus helps in understanding cell type-specific chromatin accessibility from a heterogeneous cell population.
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 is 10X?
- What are single-cell ATAC fragments and MTX files?
- What is an Anndata file, and why is it important?
Learning Objectives
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix formats
- Create a high-quality count matrix starting from scATAC-seq FASTQ files
Licence: Creative Commons Attribution 4.0 International
Keywords: 10x, Single Cell, epigenetics
Target audience: Students
Resource type: e-learning
Version: 8
Status: Active
Prerequisites:
- Introduction to Galaxy Analyses
- Pre-processing of 10X Single-Cell RNA Datasets
Learning objectives:
- Demultiplex single-cell FASTQ data from 10X Genomics
- Learn about transparent matrix formats
- Create a high-quality count matrix starting from scATAC-seq FASTQ files
Date modified: 2024-07-11
Date published: 2023-04-24
Contributors: Pavankumar Videm
External resources:
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