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

Application deadline is 30st October

Due to the current situation with covid-19, this training will be organised as a virtual workshop. The Lecture session will be recorded and made available online.

Workshop materials:

Workshop Date:

  • Session 1: Lecture, 12th November 2020, 9:30-12:00
  • Session 2: 25 min one-to-one session, 19th November 2020, 9:00-14:00 (upon request)

How to apply:

  1. Please write a short message (<200 words) to Linda Milne ( with some details about what kind of data you may be analysing.
  2. The one-to-one session is upon request. It aims to help the research groups to solve the issues of 3D RNA-seq analysis on their own datasets. Currently, we have allocated 8 one-to-one session, each with 25 minutes. Depending on the demand, extra sessions could be arranged.
  3. After the meeting we will publish all meeting presentations on the JHI ICS website (

Workshop summary

RNA-seq has been widely used for differential gene expression (DE) and alternative splicing (DAS) analysis. However, currently the analysis has been the bottleneck for most of the experiments 1) RNA-seq data analysis requires a highly specialised skillset, e.g. understanding of statistical analysis and running command lines on high performance compute; 2) It takes months to get results; 3) Out-of-date or flawed methods for RNA-seq analysis are still routinely used; 4) Lack of control of the parameters and intermediate results; and 5) Most RNA-seq analyses only focus on gene level analysis ignoring the importance of alternative splicing.

Researchers at the James Hutton Institute and the University of Dundee-Plant Sciences have developed the 3D RNA-seq App ( for biologists to implement complex DE and DAS analysis only with “clicking mouse”.

  •  The 3D App includes both DE and DAS analysis. It works for RNA-seq data from plant, animals, human, etc.
  •  It is very accurate and has good controls of false positives.
  •  It is very flexible for complex experimental design, such as time-series and developmental-series.
  •  The entire analysis only takes 1-2 hours to generate publication-quality figures, tables and reports.

3D RNA-seq App can be applied universally to all species and has been used for Arabidopsis, rice, potato, barley, human, mouse, Drosophila, plant nematodes, Phytophthora, water flea, etc. It will be highly relevant to plant and food health and animal disease and treatment studies across the SRP/Portfolio.

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.

Workshop Schedule

Day1: 12 November, Thursday Lecture
9:30 Welcome
09:35-10:05 Reference transcriptome and transcript quantification (Runxuan Zhang)
10:05-10:30 Demo: Galaxy transcript quantification (Wenbin Guo)
10:30-10:40 Break
10:40-11:20 Demo: 3D RNA-seq analysis (Wenbin Guo)
11:20-11:40 Demo: FQA
11:40-12:00 Q&A

Notes: This virtual lecture session will be recorded and made available online after the workshop.

Day 2: 19 November, Thursday One-to-one session, reservation required

(Wenbin & Runxuan)

9:00-9:25 One-to-one session 1
9:30-9:55 One-to-one session 2
10:00-10:25 One-to-one session 3
10:30-10:55 One-to-one session 4
11:00-11:25 One-to-one session 5
11:30-11:55 One-to-one session 6
13:00-13:25 One-to-one session 7
13:30-13:55 One-to-one session 8

Note: one-to-one session is upon request.


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