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Keywords: Exploratory-analysis  or metagenomics  or RNA-seq  or Genomics 


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
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
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
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
Variants: alignment and pre-treatment; GATK

DNA-seq Bioinformatics Analysis: from raw sequences to processed alignments

Keywords: DNA-seq, Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk-d2d0443e-60d2-48f0-bbec-53b94eb5b003 DNA-seq Bioinformatics Analysis: from raw sequences to processed alignments DNA-seq, Genomics
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
Exploring Microscope Platform

How to use the Microscope Platform to annotate and analyze microbial genomes.

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics

Exploring Microscope Platform https://tess.elixir-europe.org/materials/exploring-microscope-platform How to use the Microscope Platform to annotate and analyze microbial genomes. Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics
RNA-Seq: isoform detection and quantification

transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it...

Keywords: Isoforms, RNA-seq, Transcriptomics

RNA-Seq: isoform detection and quantification https://tess.elixir-europe.org/materials/rna-seq-isoform-detection-and-quantification transcriptome from new condition tissue-speci c transcriptome different development stages transcriptome from non model organism cancer cell RNA maturation mutant How to manage RNA-Seq data with genes subjected to di erential splicing? Is it possible to discover new isoforms? Is it possible to quantify abundance of each isoform Isoforms, RNA-seq, Transcriptomics
Variant Filtering

Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ...

Keywords: Genomics

Variant Filtering https://tess.elixir-europe.org/materials/variant-filtering Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ... Genomics
REPET: TEdenovo tutorial

The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE

Keywords: Annotation, Genomics

REPET: TEdenovo tutorial https://tess.elixir-europe.org/materials/repet-tedenovo-tutorial The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE Annotation, Genomics
NGS data exploration with the MicroScope Platform

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools

Keywords: Genomics, NGS, RNA-seq, SNP, Transcriptomics

NGS data exploration with the MicroScope Platform https://tess.elixir-europe.org/materials/ngs-data-exploration-with-the-microscope-platform Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools Genomics, NGS, RNA-seq, SNP, Transcriptomics
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 Variant calling practical session Genomics
RGP finder: prediction of Genomic Islands

Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization

Keywords: CDS, Data visualization, Genomics, RGP

RGP finder: prediction of Genomic Islands https://tess.elixir-europe.org/materials/rgp-finder-prediction-of-genomic-islands Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization CDS, Data visualization, Genomics, RGP
PASTEClassifier Tutorial

The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 )

Keywords: Genomics, Transposons

PASTEClassifier Tutorial https://tess.elixir-europe.org/materials/pasteclassifier-tutorial The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 ) Genomics, Transposons
Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

Chip-seq Analysis https://tess.elixir-europe.org/materials/chip-seq-analysis Quality, normalisation and peak calling Chip-seq, Genomics
Exploring microbiomes with the MicroScope Platform

This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational...

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics

Exploring microbiomes with the MicroScope Platform https://tess.elixir-europe.org/materials/exploring-microbiomes-with-the-microscope-platform This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational annotation of bacterial genomes: synteny Automatic functional assignation and expert annotation of genes Relational annotation of bacterial genomes: phylogenetic profiles Relational annotation of bacterial genomes: pan-genome analysis Relational annotation of bacterial genomes: metabolic pathways Syntactic re-annotation of public microbial genomes Syntactic annotation of microbial genomes Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics
REPET: TEdannot Tutorial

TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo

Keywords: Annotation, Genomics

REPET: TEdannot Tutorial https://tess.elixir-europe.org/materials/repet-tedannot-tutorial TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo Annotation, Genomics
Visualization of NGS data with IGV

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

Keywords: Data visualization, Genomics, NGS

Visualization of NGS data with IGV https://tess.elixir-europe.org/materials/visualization-of-ngs-data-with-igv Visualisation of next-gen sequencing data with Integrative Genomics Viewer Data visualization, Genomics, NGS
Differential gene expression analysis : Practical part

RNA-seq: Differential gene expression analysis practical session

Keywords: Genomics, RNA-seq

Differential gene expression analysis : Practical part https://tess.elixir-europe.org/materials/differential-gene-expression-analysis-practical-part RNA-seq: Differential gene expression analysis practical session Genomics, RNA-seq
RNA-seq: Differential gene expression analysis

Transcriptome analysis provides information about the identity and quantity of all RNA molecules

Keywords: Genomics, RNA-seq

RNA-seq: Differential gene expression analysis https://tess.elixir-europe.org/materials/rna-seq-differential-gene-expression-analysis Transcriptome analysis provides information about the identity and quantity of all RNA molecules Genomics, RNA-seq
Isoform discovery and quanti cation from RNA-Seq data

Not available

Keywords: RNA-seq

Isoform discovery and quanti cation from RNA-Seq data https://tess.elixir-europe.org/materials/isoform-discovery-and-quanti-cation-from-rna-seq-data Not available RNA-seq
Galaxy III: Visualization

Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV)

Keywords: Genomics

Galaxy III: Visualization https://tess.elixir-europe.org/materials/galaxy-iii-visualization Visualization of Next Generation Sequencing Data using the Integrative Genomics Viewer (IGV) Genomics
Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a...

Keywords: metagenomics

Who is doing what on the cheese surface? Overview of the cheese microbial ecosystem functioning by metatranscriptomic analyses https://tess.elixir-europe.org/materials/who-is-doing-what-on-the-cheese-surface-overview-of-the-cheese-microbial-ecosystem-functioning-by-metatranscriptomic-analyses-55c4b5d0-ba6e-4ae0-879f-7bc27c10b3eb Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We used an iterative sensory procedure to select a simplified microbial consortium, composed of only nine species (three yeasts and six bacteria), producing the odor of Livarot-type cheese when inoculated in a sterile cheese curd. All the genomes were sequenced in order to determine the functional capacities of the different species and facilitate RNA-Seq data analyses. We followed the ripening process of experimental cheeses made using this consortium during four weeks, by metatranscriptomic and biochemical analyses. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. We next applied the same approach to investigate the activity of the microorganisms in real cheeses, namely Reblochon-style cheeses. This provided useful insights into the physiological changes that occur during cheese ripening, such as changes in energy substrates, anabolic reactions, or stresses. metagenomics 2016-12-15 2017-01-11
Soil metagenomics, potential and pitfalls

The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation)....

Keywords: metagenomics

Soil metagenomics, potential and pitfalls https://tess.elixir-europe.org/materials/soil-metagenomics-potential-and-pitfalls-04d3bb46-36ba-47c0-9993-9c7d0aacad32 The soil microorganisms are responsible for a range of critical functions including those that directly affect our quality of life (e.g., antibiotic production and resistance – human and animal health, nitrogen fixation -agriculture, pollutant degradation – environmental bioremediation). Nevertheless, genome structure information has been restricted by a large extent to a small fraction of cultivated species. This limitation can be circumvented now by modern alternative approaches including metagenomics or single cell genomics. Metagenomics includes the data treatment of DNA sequences from many members of the microbial community, in order to either extract a specific microorganism’s genome sequence or to evaluate the community function based on the relative quantities of different gene families. In my talk I will show how these metagenomic datasets can be used to estimate and compare the functional potential of microbial communities from various environments with a special focus on antibiotic resistance genes. However, metagenomic datasets can also in some cases be partially assembled into longer sequences representing microbial genetic structures for trying to correlate different functions to their co-location on the same genetic structure. I will show how the microbial community composition of a natural grassland soil characterized by extremely high microbial diversity could be managed for sequentially attempt to reconstruct some bacterial genomes. Metagenomics can also be used to exploit the genetic potential of environmental microorganisms. I will present an integrative approach coupling rrs phylochip and high throughput shotgun sequencing to investigate the shift in bacterial community structure and functions after incubation with chitin. In a second step, these functions of potential industrial interest can be discovered by using hybridization of soil metagenomic DNA clones spotted on high density membranes by a mix of oligonucleotide probes designed to target genes encoding for these enzymes. After affiliation of the positive hybridizing spots to the corresponding clones in the metagenomic library the inserts are sequenced, DNA assembled and annotated leading to identify new coding DNA sequences related to genes of interest with a good coverage but a low similarity against closest hits in the databases confirming novelty of the detected and cloned genes. metagenomics 2016-12-16 2017-01-11
Welcome message

Presentation of the workshop (Chairman: Claudine Médigue)

Keywords: metagenomics

Welcome message https://tess.elixir-europe.org/materials/welcome-message-69dc597e-f839-448f-9c9d-3622ddffd592 Presentation of the workshop (Chairman: Claudine Médigue) metagenomics 2016-12-15 2017-01-11
Sequencing 6000 chloroplast genomes : the PhyloAlps project

Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding...

Keywords: metagenomics

Sequencing 6000 chloroplast genomes : the PhyloAlps project https://tess.elixir-europe.org/materials/sequencing-6000-chloroplast-genomes-the-phyloalps-project-a2b30d75-061a-4663-a5b8-593842df23bf Biodiversity is now commonly described by DNA based approches. Several actors are currently using DNA to describe biodiversity, and most of the time they use different genetic markers that is hampering an easy sharing of the accumulated knowledges. Taxonomists rely a lot on the DNA Barcoding initiative, phylogeneticists often prefer markers with better phylogenic properties, and ecologists, with the coming of the DNA metabarcoding, look for a third class of markers easiest to amplify from environmental DNA. Nevertheless they have all the same need of the knowledge accumulated by the others. But having different markers means that the sequecences have been got from different individuals in differente lab, following various protocoles. On that base, building a clean reference database, merging for each species all the available markers becomes a challenge. With the phyloAlps project we implement genome skimming at a large scale and propose it as a new way to set up such universal reference database usable by taxonomists, phylogeneticists, and ecologists. The Phyloalps project is producing for each species of the Alpine flora at least a genome skim composed of six millions of 100bp sequence reads. From such data it is simple to extract all chloroplastic, mitochondrial and nuclear rDNA markers commonely used. Moreover, most of the time we can get access to the complete chloroplast genome sequence and to a shallow sequencing of many nuclear genes. This methodes have already been successfully applied to algeae, insects and others animals. With the new single cell sequencing methods it will be applicable to most of the unicellular organisms. The good question is now : Can we consider the genome skimming as the next-generation DNA barcode ? metagenomics 2016-12-16 2017-01-11
From Samples to Data : Assuring Downstream Analysis with Upstream Planning

Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by...

Keywords: metagenomics

From Samples to Data : Assuring Downstream Analysis with Upstream Planning https://tess.elixir-europe.org/materials/from-samples-to-data-assuring-downstream-analysis-with-upstream-planning-6fac0f49-b453-4c15-a409-9753fb27ee9b Metagenomic studies have gained increasing popularity in the years since the introduction of next generation sequencing. NGS allows for the production of millions of reads for each sample without the intermediate step of cloning. However, just as in the past, the quality of the data generate by this powerful technology depends on sample preparation, library construction and the selection of appropriate sequencing technology and sequencing depth. Here we explore the different variables involved in the process of preparing samples for sequencing analysis including sample collection, DNA extraction and library construction. We also examine the various sequencing technologies deployed for routine metagenomic analysis and considerations for their use in different model systems including humans, mouse and the environment. Future developments such as long-reads will also be discussed to provide a complete picture of important aspects prior to data analyses which play a critical role in the success of metagenomic studies. metagenomics 2017-01-11