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

Authors: Pavankumar Videm

Contributors: Björn Grüning, Cristóbal Gallardo, Helena Rasche, Mehmet Tekman, Pavankumar Videm, Timon Schlegel, Wendi Bacon


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