3D RNA-seq App – A flexible and powerful tool for analysis of RNA-seq data

Mission of the Office of Research Infrastructure is toenable and accelerate new research outcomesby optimising the provision and management of La Trobe’s research infrastructure ensuring that it is efficiently and effectively used to support our researchers, industry partners and the broader research community.Goals:•	Expand the scope of La Trobe’s capabilities and access to state-of-the-art research infrastructure to ensure adequate support for the University’s areas of research strength.•	Optimise the use of new and existing research infrastructure and capabilities.•	Build recognition of La Trobe’s research environment and facilitate opportunities for both internal and external collaborations across all campuses.•	Support La Trobe’s research outcomes and the establishment of research and industry partnership through excellence in animal research infrastructure and service.•	Proactively enhance institutional Digital Research capabilities.•	Manage data throughout the research lifecycle to enable its appropriate capture, curation, analysis, publication, discovery and reuse.

Office of Research Infrastructure

Learn how to use the 3D RNA-seq App to implement complex differential gene expression and alternative splicing analysis without coding.

AgriBio  Building, Ground floor, G.1.03 Victoria Room A

RNA-seq has been widely used for differential gene expression (DE) and alternative splicing (DAS) analysis. However, there are a number of barriers to completing the analysis: 1) RNA-seq data analysis requires a highly specialised skillset, e.g. understanding of statistical analysis and running command lines on high performance computers; 2) it takes weeks/months to get results; 3) outdated or flawed methods for RNA-seq analysis are still routinely used; 4) there is a lack of control over the parameters and intermediate results; and 5) most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 have developed the <a href="https://3drnaseq.hutton.ac.uk" target="_blank" data-msys-clicktrack="0" rel="nofollow noopener noreferrer">3D RNA-seq App</a> for biologists to implement complex DE and DAS analysis with no coding required.3D RNA-seq App includes both DE and DAS analysis, and it works for RNA-seq data from plant, animals, human, etc. It is very accurate and has good control of false positives, is very flexible for complex experimental design, such as time-series and developmental-series, and the entire analysis only takes 1-2 hours to generate publication-quality figures, tables, and reports. Workshop aims and objectives:This workshop aims to:<ul><li>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. </li><li>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.</li><li>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.</li></ul>Presented by Dr Runxuan Zhang and Dr Wenbin Guo, this promises to be a very engaging event. 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.Program:9:00 am	 Accurate and rapid transcript quantification using RNA-seq data 	10:00 am Coffee break	10:30 am Genome-wide analysis of the transcriptome: transcript quantification using Salmon and Galaxy	11:30 am Break	11:45 am Transcriptome data exploratory analysis: 3D RNA-seq App, Demo	12:30 am Lunch Break	2:00 pm 3D RNA-seq App hand-on session	3:15pm Break	3:30 pm Example of the use of 3D RNA-seq App in research &amp; Summary	4:00 pm One-to-one session (appointment required)

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