Introduction to Galaxy and Single Cell RNA Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of Single Cell RNA-seq data. You will learn how to use Galaxy for analysis, and an important Galaxy feature for iterative single cell analysis. You’ll tbe guided through the general theory of single analysis and then perform a basic analysis of 10X chromium data. For support throughout these tutorials, join our Galaxy single cell chat group on Matrix to ask questions!

New to Galaxy and/or the field of scRNA-seq? Follow this learning path to get familiar with the basics!

Licence: Creative Commons Attribution 4.0 International

Keywords: Single Cell

Authors: Wendi Bacon, Pavankumar Videm

Status: Active

Learning objectives:

Module 1: Introduction to Galaxy

Learn how to upload a file
Learn how to use a tool
Learn how to view results
Learn how to view histories
Learn how to extract and run a workflow
Learn how to share a history
Learn how to set name tags
Learn how they are propagated

Module 2: Theory of Single-Cell RNA-seq

To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
Know the types of variation in an analysis and how to control for them.
Grasp what dimension reduction is, and how it might be performed.
Be familiarised with the main types of clustering techniques and when to use them.

Module 3: Time to analyse data!

Demultiplex single-cell FASTQ data from 10X Genomics
Learn about transparent matrix formats
Understand the importance of high and low quality cells
Describe an AnnData object to store single-cell data
Explain the preprocessing steps for single-cell data
Evaluate quality of single-cell data and apply steps to select and filter cells and genes based on QC
Execute data normalization and scaling
Identify highly variable genes
Construct and run a dimensionality reduction using Principal Component Analysis
Perform a graph-based clustering for cells
Identify marker genes for the clusters
Construct and run a cell type annotation for the clusters

Module 1: Introduction to Galaxy [and Single Cell RNA Sequence analysis]

• beginner 2 materials

Get a first look at the Galaxy platform for data analysis. We start with a short introduction (video slides & practical) to familiarize you with the Galaxy interface, and then proceed with a short tutorial of how to tag - and organise! - your history.

Time estimation: 1 hour

Module 2: Theory of Single-Cell RNA-seq

•• intermediate 1 material

When analysing sequencing data, you should always start with a quality control step to clean your data and make sure your data is good enough to answer your research question. After this step, you will often proceed with a mapping (alignment) or genome assembly step, depending on whether you have a reference genome to work with.

Time estimation: 30 minutes