• Event
  • Scientific training

CyVerse UK RNASeq Workshop 2018

This meeting is focused on researchers who are either at the beginning of their studies or have moved onto a new subject area and will be analysing RNAseq expression data as part of their studies.

Start date:

10 December 2018

End date:

12 December 2018

Time:

09h00 - 17h00

Venue:

Darwin Room, Earlham Institute

Organiser:

Registration deadline:

30 November 2018

Cost:

£80 for the full three-day course, including Data Carpentry on Monday 10 December, £60.00 (Sponsored by GARNet and COPO) for the two-day CyVerse and Open Data workshop. Accommodation available at £68.40 per night Bed and Breakfast.

About the event.

What is this workshop about?

This meeting is focused on researchers who are either at the beginning of their studies or have moved onto a new subject area and will be analysing RNAseq expression data as part of their studies. This workshop is designed for non-bioinformatic experts and will be run at a level appropriate for wet-lab researchers without previous bioinformatics experience. We will provide hands-on sessions that will describe the use of software tools that can interrogate RNAseq data and the biological relevance of these tools. The workshop will also demonstrate different ways to visualise RNAseq data. Prior to the workshop we will provide an example dataset that will be analysed as part of the workshop. This hands-on training will be useful for the analysis of delegates’ own data. In addition we include a session on Open Data and data reuse strategies that can benefit your research.

We are also offering a optional one-day Genomics Data Carpentry (Monday December 10) for researchers who have limited or no previous command-line experience. This optional section will introduce you to analysing data in R, and better prepare you for future analyses. The cost of this additional session is £20 to cover food, refreshments and administration.

What will I learn?

This workshop will aim to;

  • Provide delegates with data carpentry skills in the key tools needed for the analysis of RNAseq data
  • Introduce delegates to a set of available tools for analysis of RNAseq data. These include:
    - Kallisto Transcript Quantification
    - Data exploration using R with Sleuth
    - Tools for analysis of time course data
    - Analysis of alternative splicing in expression data
  • Explain the biological relevance of the RNAseq analysis software
  • Discuss the importance of Open Data and how it can benefit the research community

Who is the workshop for?

Primarily this workshop is aimed at PhD students, early career PostDoctoral researchers, but can be useful for any researcher at any level embarking on an RNAseq project.

What are the prerequisites for the workshop?

As a delegate, you are expected to be at the planning or early stages of an RNAseq project. You will be required to bring your own laptop computer as you will be handling the data analysis in the comfort of your own set-up.In additon, you will need to have set yourself up a CyVerse Account. Please register for CyVerse here.

Spaces available

40 delegates

Programme.

Day 1 - 10 December 2018

Time

Topic

09:00 - 09:30

Arrival and registration

09:30 - 10:30

Good Data Management Practices and Introduction to R and RStudio

10:30 - 11:00

Coffee

11:00 - 13:00

Working with data frames and tidyverse tools

13:00 - 14:00

Lunch

14:00 - 15:30

Working with data frames and tidyverse tools cont’d

15:30 - 16:00

Coffee

16:00 - 17:00

Visualisation in R

Day 2 - 11 December 2018

Time

Topic

09:00 - 09:30

Arrival and registration

09:30 - 10:00

Hands-on Introduction to CyVerse and CyVerseUK

10:00 - 10:30

Introducing data into the CyVerse repository

10:30 - 11:00

Coffee

11:00 - 13:00

Introduction to methodologies available for analysis of global RNA samples and explaining the biological relevance of RNAseq outputs

13:00 - 14:00

Lunch

14:00 - 15:30

Using the Kallisto-Sleuth RNAseq analysis pipeline within the CyVerse environment

15:30 - 16:00

Coffee

16:00 - 19:30

Hands-on demonstration: Data wrangling and intro to RNA-Seq with Kallisto

19:30 - 22:00

Workshop dinner, Georgian Town House (private dining)

Day 3 - 12 December 2018

Time

Topic

09:00 - 09:30

Arrival coffee

09:30 - 10:30

Open Data
- What is Open Data?
- Planning your research to deal with big data
- Where can you deposit your data?

09:30 - 10:30

Introducing COPO and how you can use it

10:30 - 11:00

Coffee

11:00 - 11:30

How reusing data can benefit your research
- Strategies for data reuse

11:30 - 12:00

Examples of successful data reuse
-Cristobal Uauy group (John Innes Centre)

12:00 - 13:00

Lunch

13:00 - 14:00

Hands-on session:
RNA-Seq data exploration in R with Sleuth (Atmosphere)

14:00 - 15:30

Updating gene expression analysis to the transcript level using RNA-seq

Hands-on session:
Flexible and powerful Differential Expression and Differential Alternative Splicing analysis using the new, user-friendly 3D RNA-seq package

15:30 - 16:00

Coffee

16:00 - 17:00

Hands-on: Introducing Earlham Institute web resources

17:00 - 17:00

Close of day 3

Further information.

This workshop is kindly sponsored by:

GARNet logo

The workshop dinner is sponsored by:

COPO logo

Fees and accommodation.

Registration for the CyVerse workshop (Tuesday 11 to Wednesday 12th December) includes lunch, refreshments, course dinner and access to all the training materials.

If you wish to attend the Data Carpentry workshop on Monday 10th December, this is an additional £20 to cover lunch, refreshments and administration.

Accommodation is available at an additional cost of £68.40 per person per  night (Bed and Breakfast rate) at Broadview Lodge, UEA.

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