Transcriptomics

Training material for all kinds of transcriptomics analysis.

Requirements

Before diving into this topic, we recommend you to have a look at:

• Introduction to Galaxy Analyses
• Sequence analysis
  • Quality Control: slides slides - tutorial hands-on
  • Mapping: slides slides - tutorial hands-on

Material

Introduction

Start here if you are new to RNA-Seq analysis in Galaxy

End-to-End Analysis

These tutorials take you from raw sequencing reads to pathway analysis

Visualisation

Tutorials covering data visualisation

Other

Assorted Tutorials

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/transcriptomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

Bérénice Batut

Maria Doyle

Florian Heyl

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Anton Nekrutenko

Matti Hoch

Clemens Blank

Lucille Delisle

Saskia Hiltemann

Pavankumar Videm

Marek Ostaszewski

Anna Trigos

Florian Heyl

Xavier Garnier

Nicola Soranzo

Cristóbal Gallardo

Maria Doyle

Anne Siegel

Daniel Maticzka

Markus Wolfien

Anika Erxleben

Charity Law

Myrthe van Baardwijk

Bérénice Batut

Peter van Heusden

Björn Grüning

Sanjay Kumar Srikakulam

Xi Liu

Mallory Freeberg

Beatriz Serrano-Solano

Jovana Maksimovic

Fotis E. Psomopoulos

Matt Ritchie

Sofoklis Keisaris

The Carpentries

Mo Heydarian

Anthony Bretaudeau

Gildas Le Corguillé

Helena Rasche

James Taylor

Iacopo Cristoferi

Olivier Dameron

Belinda Phipson

IGC Bioinformatics Unit

Chao Zhang

Shian Su

Andrea Bagnacani

Mateo Boudet

Harriet Dashnow

Toby Hodges

Erwan Corre

Mira Kuntz

José Manuel Domínguez

Funders

This material was funded by:

Gallantries

BeYond-COVID

References

• Shirley Pepke et al: Computation for ChIP-seq and RNA-seq studies
• Paul L. Auer & R. W. Doerge: Statistical Design and Analysis of RNA Sequencing Data
  Insights into proper planning of your RNA-seq run! To read before any RNA-seq experiment!
• Ian Korf: Genomics: the state of the art in RNA-seq analysis
  A refreshingly honest view on the non-trivial aspects of RNA-seq analysis
• Marie-Agnès Dillies et al: A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
  Systematic comparison of seven representative normalization methods for the differential analysis of RNA-seq data (Total Count, Upper Quartile, Median (Med), DESeq, edgeR, Quantile and Reads Per Kilobase per Million mapped reads (RPKM) normalization)
• Franck Rapaport et al: Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
  Evaluation of methods for differential gene expression analysis
• Charlotte Soneson & Mauro Delorenzi: A comparison of methods for differential expression analysis of RNA-seq data
• Adam Roberts et al: Improving RNA-Seq expression estimates by correcting for fragment bias
• Manuel Garber et al: Computational methods for transcriptome annotation and quantification using RNA-seq
  Classical paper about the computational aspects of RNA-seq data analysis
• Cole Trapnell et al: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
• Zhong Wang et al: RNA-Seq: a revolutionary tool for transcriptomics
• Dittrich, M. T. and Klau, G. W. and Rosenwald, A. and Dandekar, T. and Muller, T.: Identifying functional modules in protein-protein interaction networks: an integrated exact approach
• May, Ali; Brandt, Bernd W; El-Kebir, Mohammed; Klau, Gunnar W; Zaura, Egija; Crielaard, Wim; Heringa, Jaap; Abeln, Sanne: metaModules identifies key functional subnetworks in microbiome-related disease
• Pavankumar, Videm; Dominic, Rose; Fabrizio, Costa; Rolf, Backofen: BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles