Training material for all kinds of transcriptomics analysis.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.


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



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


Tutorials covering data visualisation

Lesson Slides Hands-on Recordings Input dataset Workflows
RNA Seq Counts to Viz in R
Visualization of RNA-Seq results with CummeRbund
Visualization of RNA-Seq results with Volcano Plot
Visualization of RNA-Seq results with Volcano Plot in R
Visualization of RNA-Seq results with heatmap2


Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
CLIP-Seq data analysis from pre-processing to motif detection
Differential abundance testing of small RNAs
GO Enrichment Analysis
Genome-wide alternative splicing analysis
Network analysis with Heinz
RNA-RNA interactome data analysis
RNA-Seq analysis with AskOmics Interactive Tool
RNA-seq Alignment with STAR
Small Non-coding RNA Clustering using BlockClust
Whole transcriptome analysis of Arabidopsis thaliana

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

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.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoAvatarBérénice Batutorcid logoAvatarMaria Doyleorcid logoAvatarFlorian Heyl

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


This material was contributed to by:

AvatarOlivier Dameronorcid logoAvatarFotis E. PsomopoulosAvatarAnna Trigosorcid logoAvatarAnthony BretaudeauAvatarIGC Bioinformatics UnitAvatarMatt Ritchieorcid logoAvatarHelena RascheAvatarJovana Maksimovicorcid logoAvatarSaskia HiltemannAvatarXavier Garnierorcid logoAvatarMallory Freebergorcid logoAvatarBeatriz Serrano-Solanoorcid logoAvatarPavankumar Videmorcid logoAvatarLucille Delisleorcid logoAvatarCristóbal Gallardoorcid logoAvatarFlorian HeylAvatarShian Suorcid logoAvatarPeter van Heusdenorcid logoAvatarBérénice Batutorcid logoAvatarNicola Soranzoorcid logoAvatarErwan CorreAvatarChao ZhangAvatarAnne Siegelorcid logoAvatarMaria DoyleAvatarAnton NekrutenkoAvatarDaniel Maticzkaorcid logoAvatarSofoklis Keisarisorcid logoAvatarMo HeydarianAvatarBelinda PhipsonAvatarThe CarpentriesAvatarCharity LawAvatarXi LiuAvatarMarkus WolfienAvatarAndrea Bagnacaniorcid logoAvatarMateo Boudetorcid logoAvatarToby HodgesAvatarGildas Le Corguilléorcid logoAvatarAnika Erxlebenorcid logoAvatarClemens BlankAvatarHarriet DashnowAvatarJames Taylor


This material was funded by:

AvatarErasmus+ Programme