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Using Galaxy

Galaxy is an open, web-based platform for data intensive biomedical research. Through its web interface, a user with no previous programming experience can design complex pipelines and deploy them on a HPC facility using the full capability of the supercomputer or Cloud resources. GenAP offers the ability to use your own privately accessed Galaxy instance, loaded with 600+ preinstalled tools. The GenAP Galaxy is fully integrated with the GenAP infrastructure, allowing users to leverage storage and compute resources as well as interact with other GenAP applications.

Below you will find quick links to a list of useful tutorials, mainly developed by the Galaxy community, covering themes such as how to get started, how to manipulate data and user interface and other features. You will also find more advanced scientific tutorials on Genome Assembly, Transcriptomics, Sequence Analysis and other subjects.

Galaxy-GenAP Basics

Lesson Wiki
Galaxy on GenAP (Overview)
File Transfer on GenAP Galaxy

Galaxy Basics

Lesson Slides Hands-on Inputs
Introduction to Galaxy
A short introduction to Galaxy
Galaxy 101
NGS data logistics

Data Manipulation

Lesson Slides Hands-on Inputs
Collections: Multisample Analysis
Collections: Rule Based Uploader
Name tags for following complex histories
Group tags for complex experimental designs

User Interface and Features

Lesson Slides Hands-on Inputs
Histories: Understanding Galaxy history system
Workflows: Extracting Workflows from Histories
Workflows: Using Workflow Parameters

Scientific Analysis


Assembly

Lesson Slides Hands-on Inputs
Introduction to Genome Assembly
Making sense of a newly assembled genome
Unicycler Assembly
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

Genome Annotation

Lesson Slides Hands-on Inputs
Introduction to Genome Annotation
Essential genes detection with Transposon insertion sequencing
Genome annotation with Maker
Genome annotation with Prokka

Sequence analysis

Lesson Slides Hands-on Inputs
Mapping
Quality Control

Transcriptomics

Lesson Slides Hands-on Inputs
Introduction to Transcriptomics
De novo transcriptome reconstruction with RNA-Seq
Differential abundance testing of small RNAs
GO Enrichment Analysis
RNA-RNA interactome data analysis
RNA-Seq reads to counts
RNA-seq counts to genes
RNA-seq genes to pathways
Reference-based RNA-Seq data analysis
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with heatmap2

Variant Analysis

Lesson Slides Hands-on Inputs
Introduction to Variant analysis
Calling variants in diploid systems
Calling variants in non-diploid systems
Exome sequencing data analysis for diagnosing a genetic disease
Identification of somatic and germline variants from tumor and normal sample pairs
Mapping and molecular identification of phenotype-causing mutations
Microbial Variant Calling


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Last updated: Wed Jun 15 2022 (prod:f1ce485b)
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