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 |
|---|---|---|---|---|---|
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Introduction to Transcriptomics
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| Reference-based RNA-Seq data analysis | |||||
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De novo transcriptome reconstruction with RNA-Seq
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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.
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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:
Bérénice Batut
Myrthe van Baardwijk
Saskia Hiltemann
Pavankumar Videm
Xi Liu
Tristan Reynolds
Hans-Rudolf Hotz
Graeme Tyson
Anika Erxleben
Simon Bray
Ekaterina Polkh
Anne Fouilloux
Anthony Bretaudeau
IGC Bioinformatics Unit
Sanjay Kumar Srikakulam
Lucille Delisle
Marek Ostaszewski
Wolfgang Maier
Toby Hodges
Daniel Maticzka
Armin Dadras
Amirhossein Naghsh Nilchi
Olivier Dameron
Mateo Boudet
Maria Doyle
Marius van den Beek
Beatriz Serrano-Solano
Charlotte Adang
Jovana Maksimovic
Peter van Heusden
Xavier Garnier
Teresa Müller
Mateusz Kuzak
Linelle Abueg
Niall Beard
Mallory Freeberg
Fotis E. Psomopoulos
Peter-Bram 't Hoen
Helena Rasche
Cristóbal Gallardo
Anton Nekrutenko
Andrea Bagnacani
William Durand
Anne Siegel
Iacopo Cristoferi
James Taylor
Casper de Visser
José Manuel Domínguez
Belinda Phipson
Clea Siguret
Erwan Corre
Sofoklis Keisaris
Mo Heydarian
Björn Grüning
Anna Trigos
Nicola Soranzo
Mira Kuntz
Mehmet Tekman
Chao Zhang
Martin Čech
Harriet Dashnow
Gildas Le Corguillé
Shian Su
Clemens Blank
Markus Wolfien
Florian Heyl
Charity Law
Matt Ritchie
Matti Hoch
Funding
These individuals or organisations provided funding support for the development of this resource
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.
The University of Melbourne
Australian BioCommons
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)
de.NBI
Melbourne Bioinformatics
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