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ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
Chip-seq: Motif Analysis Tutorial

Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, Motif analysis, NGS, Pattern recognition

Chip-seq: Motif Analysis Tutorial https://tess.elixir-europe.org/materials/chip-seq-motif-analysis-tutorial Introduction Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, Motif analysis, NGS, Pattern recognition
Chip-seq: Functional Annotation tutorial

Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms.

Keywords: Chip-seq, Functional Annotation, NGS

Chip-seq: Functional Annotation tutorial https://tess.elixir-europe.org/materials/chip-seq-functional-annotation-tutorial Global Objective Given a set of ChIP-seq peaks annotate them in order to find associated genes, genomic categories and functional terms. Chip-seq, Functional Annotation, NGS
PacBio de novo genome assembly - Hands on exercise

- Produce an assembled genomes from read file(s). - Produce genomes with : --– the awaited length, – few errors (INDELs). - Use different software packages to produce the genomes. - Understand the command line structure and some of the parameters used by the assemblers. - Polish the genome...

Resource type: PDF

PacBio de novo genome assembly - Hands on exercise https://tess.elixir-europe.org/materials/pacbio-de-novo-genome-assembly-hands-on-exercise - Produce an assembled genomes from read file(s). - Produce genomes with : --– the awaited length, – few errors (INDELs). - Use different software packages to produce the genomes. - Understand the command line structure and some of the parameters used by the assemblers. - Polish the genome to have good quality sequence.
Genome assembly with long reads

- News - PacBio read production and error patterns - Nanopore read production and error patterns - Assembly strategies - Assembly results - Conclusions

Resource type: PDF

Genome assembly with long reads https://tess.elixir-europe.org/materials/genome-assembly-with-long-reads - News - PacBio read production and error patterns - Nanopore read production and error patterns - Assembly strategies - Assembly results - Conclusions
RNA - Seq de novo

Practical session on transciptome de novo assembly

Keywords: RNA-seq

RNA - Seq de novo https://tess.elixir-europe.org/materials/rna-seq-de-novo Practical session on transciptome de novo assembly RNA-seq
Galaxy: Initiation II

Galaxy II: common tools, quality control; alignment; data managment

Keywords: Genomics

Galaxy: Initiation II https://tess.elixir-europe.org/materials/galaxy-initiation-ii Galaxy II: common tools, quality control; alignment; data managment Genomics
A Simple Phylogenetic Tree Construction (part 2)

Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

Keywords: Phylogenetics

A Simple Phylogenetic Tree Construction (part 2) https://tess.elixir-europe.org/materials/a-simple-phylogenetic-tree-construction-part-2 Understand the method used in identifying an unknown sequence. Understand the limitations of this method Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot) Phylogenetics
The IFB cloud for bioinformatics

Practical work to introduce basic and advanced usage of the IFB cloud Howto launch virtual machines Managing your data in the cloud ; Howto to connect to your VMS (SSH, web, remote desktop) Personalizing your VMs (approver, galaxy, docker)

Keywords: Cloud computing, Virtual machine

The IFB cloud for bioinformatics https://tess.elixir-europe.org/materials/the-ifb-cloud-for-bioinformatics Practical work to introduce basic and advanced usage of the IFB cloud Howto launch virtual machines Managing your data in the cloud ; Howto to connect to your VMS (SSH, web, remote desktop) Personalizing your VMs (approver, galaxy, docker) Cloud computing, Virtual machine
x2Go

Opening an x2go session to the IFBcloud

Keywords: Cloud

x2Go https://tess.elixir-europe.org/materials/x2go Opening an x2go session to the IFBcloud Cloud
Exercices on Galaxy: metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Exercices on Galaxy: metagenomics https://tess.elixir-europe.org/materials/exercices-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

Differential analysis of RNA-Seq data https://tess.elixir-europe.org/materials/differential-analysis-of-rna-seq-data Design, describe, explore and model Genomics, RNA-seq
Genomic copy number Tutorial

We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37).

Keywords: Copy number, Structural genomics

Genomic copy number Tutorial https://tess.elixir-europe.org/materials/genomic-copy-number-tutorial We will analyze the copy number variations of a human tumor (parotid gland carcinoma), limited to the chr17, from a WES (whole-exome sequencing) experiment. All genomic coordinates correspond to the 2009 build of the reference human genome (hg19 / GRC37). Copy number, Structural genomics
Galaxy Visualisation - Tutorial

Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in...

Keywords: Youri Hoogstrate

Galaxy Visualisation - Tutorial https://tess.elixir-europe.org/materials/galaxy-visualisation-tutorial Visualizations may be very helpful in understanding data better. There is a whole range of visualizations, from rather simple scatter and barplots up to projections of high dimensional data or even entire genomes. Many of these visualizations often require a lot of tweaking and changes in settings like zooming in and assigning colors, etc. Therefore, visualizations are ideally interactive, and changing settings is often an initial step in exploring data. For this reason it may be inconvenient to make use of static galaxy tools because it lacks these interactive features. For these situations Galaxy offers the option to create visualizations plugins, file format specific javascripts that integrate with the history menu, without making redundant copies of data. In this tutorial we shall go through how this system works and create a simple visualization plugin. The tool will create a visualization of the number of aligned reads per chromosome of a BAM file, and we will discuss possible optimizations and advantages and disadvantages of the proposed implementation. Youri Hoogstrate
ToolShed upload and tool-iuc PR

Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a...

Keywords: Galaxy

ToolShed upload and tool-iuc PR https://tess.elixir-europe.org/materials/toolshed-upload-and-tool-iuc-pr Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a Galaxy instance Be able to publish tools with Planemo Galaxy
Variant Filtering

Use cases: Extact a subset of variants Combine variants from several analysis Compare obtained variants from several data types Identify new variants compare to a reference list Apply specific filters for Chip Design

Keywords: NGS, Variant calling

Variant Filtering https://tess.elixir-europe.org/materials/variant-filtering-98171288-9eb3-49d3-b627-8ae1ead26885 Use cases: Extact a subset of variants Combine variants from several analysis Compare obtained variants from several data types Identify new variants compare to a reference list Apply specific filters for Chip Design NGS, Variant calling
Statistics with RStudio

Introduction to statistics with R

Keywords: R

Statistics with RStudio https://tess.elixir-europe.org/materials/statistics-with-rstudio Introduction to statistics with R R
Docker tutorial: Gene regulation

Get started with Docker! Create a Docker account Install Docker on your local host Create shared repositories and download source data Fetch the Docker image and run it with shared folders Execute the pipeline JVH / Mac

Keywords: Docker, Gene regulation

Docker tutorial: Gene regulation https://tess.elixir-europe.org/materials/docker-tutorial-gene-regulation Get started with Docker! Create a Docker account Install Docker on your local host Create shared repositories and download source data Fetch the Docker image and run it with shared folders Execute the pipeline JVH / Mac Docker, Gene regulation
DNA-seq analysis: From raw reads to processed alignments

Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling

Keywords: Alignment, DNA-seq, Genomics, Variant calling

DNA-seq analysis: From raw reads to processed alignments https://tess.elixir-europe.org/materials/dna-seq-analysis-from-raw-reads-to-processed-alignments Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling Alignment, DNA-seq, Genomics, Variant calling
DNA - seq Bioinformatics Analysis

Detection of Copy Number Variations

Keywords: DNA-seq

DNA - seq Bioinformatics Analysis https://tess.elixir-europe.org/materials/dna-seq-bioinformatics-analysis Detection of Copy Number Variations DNA-seq
Chip-seq: Pattern Analysis tutorial

Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls

Keywords: Chip-seq, NGS, Pattern recognition

Chip-seq: Pattern Analysis tutorial https://tess.elixir-europe.org/materials/chip-seq-pattern-analysis-tutorial Goal The aim is to : Get familiar with motif analysis of ChIP-seq data. Learn de novo motif discovery methods. In practice : Motif discovery with peak-motifs Differential analysis Random controls Chip-seq, NGS, Pattern recognition
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk-d2d0443e-60d2-48f0-bbec-53b94eb5b003 Variant calling practical session Genomics
Welcome and Introduction

Introduction message of the EGDW 2017

Welcome and Introduction https://tess.elixir-europe.org/materials/welcome-and-introduction Introduction message of the EGDW 2017
Variant annotation

Add meta-information on variant to facilitate interpretation

Keywords: Variant analysis

Variant annotation https://tess.elixir-europe.org/materials/variant-annotation Add meta-information on variant to facilitate interpretation Variant analysis
RNA-Seq: Differential Expression Analysis

Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13...

Keywords: Differential Expression, RNA-seq, transcriptomics

RNA-Seq: Differential Expression Analysis https://tess.elixir-europe.org/materials/rna-seq-differential-expression-analysis Be careful about experimental design : avoid putting all the replicates in the same lane, using the same barcode for the replicates, putting different number of samples in lanes etc... Non- uniformity of the per base read distribution (Illumina Random Hexamer Priming bias visible on the 13 first bases) Bias hierarchy : biological condition concentration run/flowcell lane At equivalent expression level, a long gene will have more reads than a short one. Non random coverage along the transcript. Multiple hit for some reads alignments. Differential Expression, RNA-seq, transcriptomics
Eukaryotic small RNA

Small RNAseq data analysis for miRNA identification

Keywords: RNA-seq

Eukaryotic small RNA https://tess.elixir-europe.org/materials/eukaryotic-small-rna Small RNAseq data analysis for miRNA identification RNA-seq
Third generation sequencing : the revolution of long reads

Introduction on sequencing: available technologies, library types, applications ...

Keywords: Genomics

Third generation sequencing : the revolution of long reads https://tess.elixir-europe.org/materials/third-generation-sequencing-the-revolution-of-long-reads Introduction on sequencing: available technologies, library types, applications ... Genomics
BioBlend API

BioBlend module, a python library to use Galaxy API

Keywords: API, Galaxy, Python

BioBlend API https://tess.elixir-europe.org/materials/bioblend-api BioBlend module, a python library to use Galaxy API API, Galaxy, Python
Snakemake tutorial: Gene regulation

Workflow 1: Rules and targets Workflow 2: Introducing wildcards Workflow 3: Keywords Workflow 4: Combining rules Workflow 5: Configuration file Workflow 6: Separated files

Keywords: Gene regulation, Snakemake

Snakemake tutorial: Gene regulation https://tess.elixir-europe.org/materials/snakemake-tutorial-gene-regulation-60b23a0f-6878-48bf-8ef0-f4e283f7ec03 Workflow 1: Rules and targets Workflow 2: Introducing wildcards Workflow 3: Keywords Workflow 4: Combining rules Workflow 5: Configuration file Workflow 6: Separated files Gene regulation, Snakemake
A Quick and focused overview of R data types and ggplot2 syntax

R and RStudio overview.

Keywords: Graphical analysis, R, Statistics

A Quick and focused overview of R data types and ggplot2 syntax https://tess.elixir-europe.org/materials/a-quick-and-focused-overview-of-r-data-types-and-ggplot2-syntax-b0aa7b0d-f355-44d7-baed-93d124c0f3ba R and RStudio overview. Graphical analysis, R, Statistics