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
- slides Slides: Quality Control
- tutorial Hands-on: Quality Control
- slides Slides: Mapping
- tutorial Hands-on: Mapping
Material
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Introduction
Start here if you are new to RNA-Seq analysis in Galaxy
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
|
Introduction to Transcriptomics
|
|||||
| Reference-based RNA-Seq data analysis | |||||
|
De novo transcriptome reconstruction with RNA-Seq
|
End-to-End Analysis
These tutorials take you from raw sequencing reads to pathway analysis
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| 1: RNA-Seq reads to counts | |||||
| 2: RNA-seq counts to genes | |||||
| 3: RNA-seq genes to pathways |
Visualisation
Tutorials covering data visualisation
Other
Assorted Tutorials
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.
Follow topic updates rss-feed with our RSS Feed
Community Resources
Community Home Maintainer HomeEditorial Board
This material is reviewed by our Editorial Board:
Bérénice Batut
Maria Doyle
Florian Heyl
Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!
Contributors
This material was contributed to by:
Anna Trigos
Mira Kuntz
Ekaterina Polkh
José Manuel Domínguez
Martin Čech
Xavier Garnier
Mallory Freeberg
Mateusz Kuzak
Iacopo Cristoferi
Clemens Blank
William Durand
Sofoklis Keisaris
Mo Heydarian
Charity Law
Erwan Corre
Charlotte Adang
Linelle Abueg
Peter van Heusden
Simon Bray
James Taylor
Casper de Visser
Harriet Dashnow
Matt Ritchie
Daniel Maticzka
Pavankumar Videm
Florian Heyl
Anthony Bretaudeau
IGC Bioinformatics Unit
Jovana Maksimovic
Marius van den Beek
Lucille Delisle
Teresa Müller
Chao Zhang
Maria Doyle
Amirhossein Naghsh Nilchi
Toby Hodges
Armin Dadras
Graeme Tyson
Clea Siguret
Hans-Rudolf Hotz
Matti Hoch
Andrea Bagnacani
Bérénice Batut
Anne Siegel
Markus Wolfien
Beatriz Serrano-Solano
Myrthe van Baardwijk
Gildas Le Corguillé
Fotis E. Psomopoulos
Saskia Hiltemann
Peter-Bram 't Hoen
Wolfgang Maier
Olivier Dameron
Helena Rasche
Björn Grüning
Niall Beard
Mateo Boudet
Nicola Soranzo
Cristóbal Gallardo
Anika Erxleben
Mehmet Tekman
Shian Su
Belinda Phipson
Sanjay Kumar Srikakulam
Marek Ostaszewski
Anton Nekrutenko
Anne Fouilloux
Xi Liu
Funding
These individuals or organisations provided funding support for the development of this resource
de.NBI
Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.
BeYond-COVID
BY-COVID is an EC funded project that tackles the data challenges that can hinder effective pandemic response.
This project has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement № 101046203 (BY-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