Information & Computational Sciences

SEFARI Workshop: 3D RNA-seq App

3D RNA-seq App – A flexible and powerful tool for differential expression and alternative splicing analysis of RNA-seq data for biologists

UPDATE: Due to the current situation with COVID-19 this event has been cancelled until further notice. We will rearrange the event once government guidance around COVID-19 allows meetings of large groups and non-essential travel.

Please bring your own laptop (you only need a web browser).

This workshop will take place at the James Hutton Institute, Dundee site

Workshop Date: 07 May 2020.

Location: New Seminar Room, the James Hutton Institute, Invergowrie Dundee DD2 5DA Scotland.

How to apply:

  1. Please write a short message (<200 words) to Gordon Stephen ( explaining why you would like to attend this workshop.
  2. The organising team will then decide who will attend the workshop. Preference will be given to people who will be able to teach others at their host institution about use of the 3D RNAseq tool as well as to those who will be imminently analysing their own RNA-Seq data. We will inform successful applicants by April 6th, 2020 so that you can arrange your travel to and accommodation if needed.
  3. After the meeting we will publish all meeting presentations on the JHI ICS website.)

Workshop summary

Aims and Objectives

  • Empower biologists to perform complex DE and DAS analyses, enabling them to make full use of their RNA-seq data and produce experimental results in a robust, transparent and reproducible way to achieve open science. We strongly encourage early career research scientists (postdocs, PhD students) to take this opportunity to acquire the skill to analyse RNA-seq data and improve portfolios.
  • Improve the efficiency and overcome major bottleneck for wet lab biologists by training them to utilise 3D RNA-seq, which reduce the time for a complete RNA-seq experiment from 3-4 months to just a few days.
  • Raise the awareness of the importance of alternative splicing in the gene expression mechanism and the effects of high-quality transcriptome to transcript quantification and analysis.


  • How relevant to your research, e.g. currently working/plan to work on RNA-seq data
  • Willing to teach other people in your institute for 3D RNA-seq analysis

On-the-Day Details

Participants are expected to arrange their own transportation and accommodation if required. Lunch and refreshments will be provided.

Workshop Schedule

09:30 Arrival and coffee
09:55 Welcome
10:00 Runxuan Zhang: Reference transcriptome and quantification
10:45 Tea/coffee
11:00 Hands-on session: Salmon quantification on Galaxy (Gordon
12:00 Lunch and networking
12:45 Showcase talks of 3D RNA-seq, internal/external speakers
13:45 Hands-on session: 3D RNA-seq analysis (Wenbin Guo)
15:00 Tea/coffee
15:15 Hands-on session: 3D RNA-seq analysis (Wenbin Guo)
16:15 Conclusions (workshop survey)
16:30 Networking reception