Archives AVIESAN-IFB 2016 - v5

Introduction sur le séquençage: technologies disponibles, types de librairies, applications

By Thierry Grange

Accès au fichier

Les instances Galaxy pour les tutorats et cours

By Christophe Caron

Accès au fichier

Galaxy 0: Cloud IFB présentation et lancement de l'instance

By Sandrine Perrin

Accès au fichier

Galaxy I: Initation à Galaxy

By Maria Bernard

Accès au fichier

Méthodes d'alignement

By Matthias Zytnicki

Accès au fichier

Third generation sequencing : the revolution of long reads

By Claude Thermes
Introduction on sequencing: available technologies, library types, applications ...

Galaxy: Initiation II

By Gildas Le Corguillé

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


Galaxy III: Visualization

By Elodie Girard

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


Atelier Détection de Variants

By Nicolas Lapalu

Accès au fichier

Chip-seq Analysis

By Stéphanie Legras

Quality, normalisation and peak calling


Variants: alignment and pre-treatment; GATK

By Elodie Girard

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


Variants: alignment and pre-treatment; GATK

By Elodie Girard

Variant calling practical session


Variant Filtering

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

...


RNA-seq: Differential gene expression analysis

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

Differential gene expression analysis : Practical part

By Rachel Legendre

RNA-seq: Differential gene expression analysis practical session


Ligne de commande

By Denis Puthier

Accès au fichier

Differential analysis of RNA-Seq data

By Rachel Legendre

Design, describe, explore and model


Variant annotation

By Viven Deshaies
Add meta-information on variant to facilitate interpretation

DNA - seq Bioinformatics Analysis

By Elodie Girard

Detection of Copy Number Variations
 


Isoform discovery and quanti cation from RNA-Seq data

By Claire Toffano-Nioche

Not available


RADSeq Data Analysis

By Yvan Le Bras

Introduction to RADSeq through STACKS on Galaxy


x2Go

By Denis Puthier
Opening an x2go session to the IFBcloud

Transcriptome de novo assembly

By Erwan Corre

Not available


RNA - Seq de novo

By Xi Liu

Practical session on transciptome de novo assembly


Statistics with RStudio

By Jaces Van Helden

Introduction to statistics with R


Eukaryotic small RNA

By Matthias Zytnicki

Small RNAseq data analysis for miRNA identification


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