Galaxy Training

GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy.

Galaxy Training https://tess.oerc.ox.ac.uk/content_providers/galaxy-training GitHub repository and its website companion containing a collection of training materials for teaching next generation sequencing data analysis uing Galaxy. /system/content_providers/images/000/000/056/original/GTNLogo1000.png?1518085304
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Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction to Transcriptomics https://tess.oerc.ox.ac.uk/materials/transcriptomics-introduction-to-transcriptomics Training material for all kinds of transcriptomics analysis.

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - Introduction to Genome Assembly https://tess.oerc.ox.ac.uk/materials/assembly-introduction-to-genome-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How do we perform a very basic genome assembly from short read data? Objectives of the tutorial: - assemble some paired end reads using Velvet - examine the output of the assembly.

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - De Bruijn Graph Assembly https://tess.oerc.ox.ac.uk/materials/assembly-de-bruijn-graph-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - What are the factors that affect genome assembly? - How does Genome assembly work? Objectives of the tutorial: - Perform an optimised Velvet assembly with the Velvet Optimiser - Compare this assembly with those we did in the basic tutorial - Perform an assembly using the SPAdes assembler.

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome...

Assembly - Unicycler Assembly https://tess.oerc.ox.ac.uk/materials/assembly-unicycler-assembly DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.' We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone. Questions of the tutorial: - How to perform an hybrid bacterial assembly with Unicycler Objectives of the tutorial: - Perform Quality Control on your reads - Perform a Small genome Assembly with Unicycler - Evaluate the Quality of the Assembly with Quast - Annotate the assembly with Prokka

Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file -...

Sequence analysis - Quality Control https://tess.oerc.ox.ac.uk/materials/sequence-analysis-quality-control Analyses of sequences Questions of the tutorial: - How to control quality of NGS data? - What are the quality parameters to check for each dataset? - How to improve the quality of a sequence dataset? Objectives of the tutorial: - Manipulate FastQ files - Control quality from a FastQ file - Use FastQC tool - Understand FastQC output - Use tools for quality correction

Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Sequence analysis - Mapping https://tess.oerc.ox.ac.uk/materials/sequence-analysis-mapping Analyses of sequences Questions of the tutorial: - What two things are crucial for a correct mapping? - What is BAM? Objectives of the tutorial: - You will learn what mapping is - A genome browser is shown that helps you to understand your data

Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Sequence analysis - Genome Annotation https://tess.oerc.ox.ac.uk/materials/sequence-analysis-genome-annotation Analyses of sequences Questions of the tutorial: - First question addressed during the tutorial - Second question addressed during the tutorial Objectives of the tutorial: - First learning objectives of the tutorial - Second learning objectives of the tutorial

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate...

Sequence analysis - RAD-Seq de-novo data analysis https://tess.oerc.ox.ac.uk/materials/sequence-analysis-rad-seq-de-novo-data-analysis Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data without a reference genome for a population genomics study? Objectives of the tutorial: - Analysis of RAD sequencing data without a reference genome - SNP calling from RAD sequencing data - Calculate population genomics statistics from RAD sequencing data

Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software

Sequence analysis - RAD-Seq to construct genetic maps https://tess.oerc.ox.ac.uk/materials/sequence-analysis-rad-seq-to-construct-genetic-maps Analyses of sequences Questions of the tutorial: - How to analyze RAD sequencing data for a genetic map study? Objectives of the tutorial: - SNP calling from RAD sequencing data - Find and correct haplotypes - Create input files for genetic map building software

ChIP-sequencing is a method used to analyze protein interactions with DNA.

ChIP-Seq data analysis - Introduction to ChIP-Seq data analysis https://tess.oerc.ox.ac.uk/materials/chip-seq-data-analysis-introduction-to-chip-seq-data-analysis ChIP-sequencing is a method used to analyze protein interactions with DNA.

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with...

ChIP-Seq data analysis - Identification of the binding sites of the Estrogen receptor https://tess.oerc.ox.ac.uk/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-estrogen-receptor ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of the Estrogen receptor? Objectives of the tutorial: - Inspect read quality with FastQC - Map reads with Bowtie2 - Assess the quality of an ChIP-seq experiments - Extract coverage files - Call enriched regions or peaks

Train the trainers

Train the trainers - Introduction to training with Galaxy https://tess.oerc.ox.ac.uk/materials/train-the-trainers-introduction-to-training-with-galaxy Train the trainers

Train the trainers Questions of the tutorial: - How to integrate a new tutorial? - How to write a tutorial with hands-on? Objectives of the tutorial: - Creating a tutorial from scratch - Creating hands-on

Train the trainers - Creating a new tutorial - Writing content in Markdown https://tess.oerc.ox.ac.uk/materials/train-the-trainers-creating-a-new-tutorial-writing-content-in-markdown Train the trainers Questions of the tutorial: - How to integrate a new tutorial? - How to write a tutorial with hands-on? Objectives of the tutorial: - Creating a tutorial from scratch - Creating hands-on

Train the trainers Questions of the tutorial: - What does Metadata in GTN means? - Which kind of metadata can I annotate? - For what is metadata used? Objectives of the tutorial: - Adding metadata for a tutorial - Defining learning objectives

Train the trainers - Creating a new tutorial - Defining metadata https://tess.oerc.ox.ac.uk/materials/train-the-trainers-creating-a-new-tutorial-defining-metadata Train the trainers Questions of the tutorial: - What does Metadata in GTN means? - Which kind of metadata can I annotate? - For what is metadata used? Objectives of the tutorial: - Adding metadata for a tutorial - Defining learning objectives

Train the trainers Questions of the tutorial: - How to setup the infrastructure to build training webpages? Objectives of the tutorial: - Installing packages needed for rendering the webpage - Running the GTN website locally - Tracking changes to the content live in the webbrowser

Train the trainers - Creating a new tutorial - Setting up the infrastructure https://tess.oerc.ox.ac.uk/materials/train-the-trainers-creating-a-new-tutorial-setting-up-the-infrastructure Train the trainers Questions of the tutorial: - How to setup the infrastructure to build training webpages? Objectives of the tutorial: - Installing packages needed for rendering the webpage - Running the GTN website locally - Tracking changes to the content live in the webbrowser

Train the trainers Questions of the tutorial: - What is a Interactive Galaxy Tour? - How can we create an Interactive Tour? Objectives of the tutorial: - Creating a Galaxy tour from scratch - Deploying and running a tour

Train the trainers - Creating a new tutorial - Creating Interactive Galaxy Tours https://tess.oerc.ox.ac.uk/materials/train-the-trainers-creating-a-new-tutorial-creating-interactive-galaxy-tours Train the trainers Questions of the tutorial: - What is a Interactive Galaxy Tour? - How can we create an Interactive Tour? Objectives of the tutorial: - Creating a Galaxy tour from scratch - Deploying and running a tour

Train the trainers Questions of the tutorial: - What do we need to take care when running a workshop? - What are the good practices? Objectives of the tutorial: - Reflect on the things to do before, during and after a workshop

Train the trainers - Good practices to run a workshop https://tess.oerc.ox.ac.uk/materials/train-the-trainers-good-practices-to-run-a-workshop Train the trainers Questions of the tutorial: - What do we need to take care when running a workshop? - What are the good practices? Objectives of the tutorial: - Reflect on the things to do before, during and after a workshop

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Galaxy Server administration - Galaxy from an administrator point of view https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-galaxy-from-an-administrator-point-of-view Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - What options to deploy Galaxy do I have? - Which platforms are supported by Galaxy? - What requirements does Galaxy have? Objectives of the tutorial: - Learn about...

Galaxy Server administration - Deployment and Platform options https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-deployment-and-platform-options Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - What options to deploy Galaxy do I have? - Which platforms are supported by Galaxy? - What requirements does Galaxy have? Objectives of the tutorial: - Learn about different options about Galaxy deployment. - Make an educated decision about your preferred deployment model.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - How does Galaxy manage users and groups? - How can I assign Quotas to specific users/groups? Objectives of the tutorial: - Learn the Galaxy user/group management and...

Galaxy Server administration - User, Group and Quota managment https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-user-group-and-quota-managment Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - How does Galaxy manage users and groups? - How can I assign Quotas to specific users/groups? Objectives of the tutorial: - Learn the Galaxy user/group management and assign Quotas. - Understand the Role Based Access Control (RBAC) of Galaxy.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring...

Galaxy Server administration - Server Monitoring and Maintenance https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-server-monitoring-and-maintenance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - How to monitor a Galaxy service? - What are the best practices to maintain a Galaxy server? Objectives of the tutorial: - Learn about different monitoring strategies. - Setup and start the Galaxy reports app.

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that - How to...

Galaxy Server administration - Galaxy Database schema https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-galaxy-database-schema Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Running a production Galaxy server, you some times end up in with a situation, where you manually need to interact with the Galaxy database: how do you do that - How to extract usage information, which can not be gathered using the given report tools - How to move from MySQL to PostgreSQL - Is there ever a need to manually change the contents of a table Objectives of the tutorial: - Learn some of the design concepts of the Galaxy database - Extract information from the Galaxy database - Get to know SchemaSpy

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Why Docker? What is it? - How to use Docker? - How to integrate Galaxy in Docker to facilitate its deployment? Objectives of the tutorial: - Docker basics - Galaxy...

Galaxy Server administration - Docker and Galaxy https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-docker-and-galaxy Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - Why Docker? What is it? - How to use Docker? - How to integrate Galaxy in Docker to facilitate its deployment? Objectives of the tutorial: - Docker basics - Galaxy Docker image (usage) - Galaxy Docker (internals) - Galaxy flavours

Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Galaxy Server administration - Advanced customisation of a Galaxy instance https://tess.oerc.ox.ac.uk/materials/galaxy-server-administration-advanced-customisation-of-a-galaxy-instance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using...

Transcriptomics - Reference-based RNA-Seq data analysis https://tess.oerc.ox.ac.uk/materials/transcriptomics-reference-based-rna-seq-data-analysis Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Analysis of differentially expressed genes - Identification of functional enrichment among differentially expressed genes

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How are RNA-Seq results stored? - Why are visualization techniques needed? - How to select our desired subjects for differential gene expression analysis? Objectives of the tutorial: - Manage RNA-Seq...

Transcriptomics - Visualization of RNA-Seq results with CummeRbund https://tess.oerc.ox.ac.uk/materials/transcriptomics-visualization-of-rna-seq-results-with-cummerbund Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How are RNA-Seq results stored? - Why are visualization techniques needed? - How to select our desired subjects for differential gene expression analysis? Objectives of the tutorial: - Manage RNA-Seq results - Extract the desired subject for differential gene expression analysis - Visualize information

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

Transcriptomics - Reference-based RNAseq data analysis (long) https://tess.oerc.ox.ac.uk/materials/transcriptomics-reference-based-rnaseq-data-analysis-long Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How to perform analysis of RNAseq data when reference genome is available? Objectives of the tutorial: - Learns basic concepts of RNAseq analysis

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a...

Proteomics - Protein FASTA Database Handling https://tess.oerc.ox.ac.uk/materials/proteomics-protein-fasta-database-handling Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to download protein FASTA databases of a certain organism? - How to download a contaminant database? - How to create a decoy database? - How to combine databases? Objectives of the tutorial: - Creation of a protein FASTA database ready for use with database search algorithms.

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform...

Proteomics - Metaproteomics tutorial https://tess.oerc.ox.ac.uk/materials/proteomics-metaproteomics-tutorial Training material for proteomics workflows in Galaxy Questions of the tutorial: - How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data? - How can I perform taxonomy analysis and visualize metaproteomics data? - How can I perform functional analysis on this metaproteomics data? Objectives of the tutorial: - A taxonomy and functional analysis of metaproteomic mass spectrometry data.

Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.

Proteomics - Label-free versus Labelled - How to Choose Your Quantitation Method https://tess.oerc.ox.ac.uk/materials/proteomics-label-free-versus-labelled-how-to-choose-your-quantitation-method Training material for proteomics workflows in Galaxy Questions of the tutorial: - What are benefits and drawbacks of different quantitation methods? - How to choose which quantitation method bests suits my need? Objectives of the tutorial: - Choose your quantitation method.
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