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.elixir-europe.org/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/000/000/078/original/GTNLogo1000.png?1501677361
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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.elixir-europe.org/materials/analysis-of-sequences-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

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.elixir-europe.org/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

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.elixir-europe.org/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.

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.elixir-europe.org/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

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.elixir-europe.org/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.

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.elixir-europe.org/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.

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Metagenomics - Introduction https://tess.elixir-europe.org/materials/metagenomics-introduction Metagenomics is a discipline that enables the genomic study of uncultured microorganisms

Train the trainers

Train the trainers - Introduction https://tess.elixir-europe.org/materials/train-the-trainers-introduction Train the trainers

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - First question addressed during...

Introduction to Galaxy - Multisample Analysis https://tess.elixir-europe.org/materials/galaxy-introduction-multisample-analysis Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. 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 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.elixir-europe.org/materials/analysis-of-sequences-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

Training material for all kinds of transcriptomics analysis.

Transcriptomics - Introduction https://tess.elixir-europe.org/materials/transcriptomics-introduction Training material for all kinds of transcriptomics analysis.

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.elixir-europe.org/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

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Introduction to Galaxy - Introduction https://tess.elixir-europe.org/materials/galaxy-introduction-introduction Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Epigenetics - Introduction https://tess.elixir-europe.org/materials/epigenetics-introduction DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements.

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets...

Transcriptomics - Differential abundance testing of small RNAs https://tess.elixir-europe.org/materials/transcriptomics-differential-abundance-testing-of-small-rnas Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets to determine quality and reproducibility. - Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets. - Differentiate between subclasses of small RNAs based on their characteristics. - Identify differently abundant small RNAs and their targets.

DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be...

Epigenetics - DNA Methylation data analysis https://tess.elixir-europe.org/materials/epigenetics-dna-methylation-data-analysis DNA methylation is an epigenetic mechanism used by higher eukaryotes and involved in e.g. gene expression, X-Chromosome inactivating, imprinting, and gene silencing of germline specific gene and repetitive elements. Questions of the tutorial: - What is methylation and why it cannot be recognised by a normal NGS procedure? - Can a different methylation influence the expression of a gene? How? - Which tools you can use to analyse methylation data? Objectives of the tutorial: - Learn how to analyse methylation data - Get a first intuition what are common pitfalls.

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy Introduction - Visualization https://tess.elixir-europe.org/materials/galaxy-introduction-visualization Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Galaxy Introduction - Collections https://tess.elixir-europe.org/materials/galaxy-introduction-collections Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.

Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - How to analyze metagenomics data? - What information can be extracted of metagenomics data? - What is the difference between amplicon and shotgun data? - What are the difference...

Metagenomics - Analyses of metagenomics data - The global picture https://tess.elixir-europe.org/materials/metagenomics-analyses-of-metagenomics-data-the-global-picture Metagenomics is a discipline that enables the genomic study of uncultured microorganisms Questions of the tutorial: - How to analyze metagenomics data? - What information can be extracted of metagenomics data? - What is the difference between amplicon and shotgun data? - What are the difference in the analyses of amplicon and shotgun data? Objectives of the tutorial: - Choosing the best approach to analyze metagenomics data - Selection of tools to analyze amplicon data or shotgun data - Visualisation of a community structure

Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to combine two different methods for localization prediction? Objectives of the tutorial: - Use a localization prediction algorithm in Galaxy. - Extract proteins from a list of identifiers that match a...

Proteomics - Secretome Prediction https://tess.elixir-europe.org/materials/proteomics-secretome-prediction Training material for proteomics workflows in Galaxy Questions of the tutorial: - How to combine two different methods for localization prediction? Objectives of the tutorial: - Use a localization prediction algorithm in Galaxy. - Extract proteins from a list of identifiers that match a specific GO term. - Combine the results of different predictions to a final output.

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

Galaxy Server administration - Introduction https://tess.elixir-europe.org/materials/galaxy-server-administration-introduction 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: - - Objectives of the tutorial: - - -

Galaxy Server administration - Move from dev instance to production instance https://tess.elixir-europe.org/materials/galaxy-server-administration-move-from-dev-instance-to-production-instance Administration of Galaxy Servers (setting up, Docker use, databases, ...) can be a complex task Questions of the tutorial: - - Objectives of the tutorial: - - -

Exome sequencing means that all protein-coding genes in a genome are sequenced

Variant Analysis - Introduction https://tess.elixir-europe.org/materials/variant-analysis-introduction Exome sequencing means that all protein-coding genes in a genome are sequenced

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Development in Galaxy - Introduction https://tess.elixir-europe.org/materials/development-in-galaxy-introduction Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - What is a workflow? - How can I...

Introduction to Galaxy - Extracting Workflows from Histories https://tess.elixir-europe.org/materials/introduction-to-galaxy-extracting-workflows-from-histories Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - What is a workflow? - How can I create a workflow based on my analysis history? Objectives of the tutorial: - Learn how to extract a workflow from a Galaxy history - Learn how to change a workflow using the workflow editor

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.

Tutorials using public Galaxy at usegalaxy.org - NGS data logistics https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-ngs-data-logistics This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - How to manipulate and process NGS data Objectives of the tutorial: - Learn about Fastq, SAM, and BAM.

Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get...

Introduction to Galaxy - From peaks to genes https://tess.elixir-europe.org/materials/galaxy-introduction-from-peaks-to-genes Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Questions of the tutorial: - How to use Galaxy? - How to get from peak regions to a list of gene names? Objectives of the tutorial: - Familiarize yourself with the basics of Galaxy - Learn how to obtain data from external sources - Learn how to run tools - Learn how histories work - Learn how to create a workflow - Learn how to share your work

This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - What is frequency of variants is so low that it is obscured by sequencing error rate? Objectives of the tutorial: - Learn about duplex sequencing and analysis of duplex reads

Tutorials using public Galaxy at usegalaxy.org - Calling very rare variants https://tess.elixir-europe.org/materials/tutorials-using-public-galaxy-at-usegalaxy-org-calling-very-rare-variants This tutorials cover a variety of analyses that can be performed at usegalaxy.org Questions of the tutorial: - What is frequency of variants is so low that it is obscured by sequencing error rate? Objectives of the tutorial: - Learn about duplex sequencing and analysis of duplex reads

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own...

Development in Galaxy - Galaxy Interactive Environments https://tess.elixir-europe.org/materials/development-in-galaxy-galaxy-interactive-environments Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - What are Galaxy Interactive Environments (GIEs)? - How to enable GIEs in Galaxy? - How to develop your own GIE? Objectives of the tutorial: - Implement a Hello-World Galaxy Interactive Environment

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom...

Development in Galaxy - Visualizations: charts plugins https://tess.elixir-europe.org/materials/development-in-galaxy-visualizations-charts-plugins Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Questions of the tutorial: - How can I make a custom plugin for Charts? Objectives of the tutorial: - Learn how to add custom javascript plugins to the Galaxy Charts framework
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