the Power of RNA-seq

general information

Date: December 16th-18th, 2013
Location: Wageningen University, the Netherlands
Website: (This EPS website contains the same course information)
Keywords: RNA-seq, transcriptome analysis, experimental design, read mapping, quality control, differential expression, RNA-editing, interpretation, data analysis, allelic expression
Organisers: Harm Nijveen, Dick de Ridder & Edouard Severing (WUR bioinformatics laboratory), Gabino Sanchez-Perez (PRI), graduate school Experimental Plant Sciences (EPS)
Contact: Patrick Koks (WUR, NBIC), Patrick.Koks@WUR.NL
Registration:  enrolment page

Short course description

The graduate school Experimental Plant Sciences (EPS), the Bioinformatics Laboratory (WUR) and the Netherlands Bioinformatics Centre (NBIC) are organising an NGS application course on RNA-seq. This is a 3-day course that will consist of lectures in the morning and extensive hands-on computer practicals in the afternoon.
Researchers’ questions are the driving force of our programme:

• Which questions can be addressed with RNA-seq?
• How many samples and replicates do I need?
• Which steps are involved in an RNA-seq experiment?
• What is Differential Expression?
• What can go wrong?

Venue

Wageningen UR, Wageningen.

morning sessions (lectures) are in room C92
afternoon sessions (workshops) are in room PC95
both in Radix (building 107), Droevdaalsesteeg 1
6708 PB, Wageningen

Lecturers

• Edouard Severing
• Harm Nijveen
• Gabino Sanchez-Perez
• Elio Schijlen
• Paul Eilers
• Sandra Smit
• Marco Bink
• Aalt-Jan van Dijk
• Ole Madsen
• Basten Snoek
• Richard Immink

Target audience

This beginners course is intended for (post) graduate researchers and bioinformaticians who want to start applying RNA-seq analysis methods on their data tomorrow. The course is intended for people with a basic understanding in (NGS) data analysis. Previous experience with NGS or RNA-seq data analysis, R or Galaxy is not required. We do expect a reasonable computer literacy and a basic knowledge of biology, DNA-technology and statistics.

Course Description

This 3-day course will teach you many general aspects of RNA-seq during the morning lectures on NGS & RNA-seq theory, but also the context, applicability, power and expected results of RNA-seq experiments. During the practicals, you'll learn the basic steps an RNA-seq pipeline consist of, how to interpret your data and to put the results to use in your research project. We'll use Galaxy, R and webtools for this.

Day 1 consists of an introduction to RNA-seq and NGS techniques in general, followed by specialised lectures on sample preparation and quality control of your raw data. In the afternoon, Galaxy will be introduced and used for tutorials on quality control and the first steps of an RNA-seq data-analysis pipeline.

Day 2 will continue with lectures on RNA-seq and differential expression, statistical evaluation of the processed data and GO-enrichment of your results. The statistical language ‘R’ will be introduced and in the afternoon RNA-seq data are analysed using both Galaxy and R.

Day 3 focuses on special applications using transcriptome data, like RNA editing, SNP analysis and eQTL analysis. Your Galaxy proficiency will be challenged in one more tutorial on RNA editing, followed by a wrap –up. The course will be concluded with drinks.

The afternoons of all 3 days are reserved for workshops. Real though size-limited data-sets will be used where possible in hands-on tutorials using open source software.

topics

• Experimental design
• Sequencing requirements
• Biological applications
• An RNA-seq data analysis pipeline (quality control, mapping, identification, quantification)
• Differential expression
• Use cases

Format

workshops:

• General introductions in R and Galaxy
• Data quality control (Galaxy)
• Data quality control in a statistical perspective (R)
• RNA-seq data analysis pipeline (R)
• RNA-seq data analysis pipeline (Galaxy)
• RNA-editing (Galaxy)

Registration

You can apply for this course at this page.
There is a maximum number of 35 seats available for this course. After notification of your application you will receive a confirmation of attendance before December 1st or within 2 weeks after your application. 20 Seats for this course will be reserved for members of EPS until December 1st. After that date, all seats will be available for anyone interested.

Registration

All 35 available seats for this course are full.

You may fill in the pre-registration form here to inform us of your interest in the next edition of this course. A date (presumably medio 2014) has not been determined yet.

For the lectures during the morning sessions we have a bigger lecture room. Please contact Patrick.Koks@removethis.wur.nl for availability if you want to attend these.

Course preparations

For the (afternoon) computer workshops, we will use standard Windows-desktops using a webbrowser for remote access to a local instance of Galaxy in Wageningen (the main, public Galaxy server is here: https://usegalaxy.org/). Access to the local server and demo files will be arranged on the first day of the course.

For the R-workshops, we will use local installations in the computer room using RStudio for easier interaction with 'R'. For the absolute beginner 'R' may look a bit challengeing, but we will introduce you gently. Still, a bit of practicing before the start of the course will give you a head-start. For this I've included a very short and easy tutorial (see this pdf on the R-website). Following this tutorial, you will install the latest versions of R and RStudio (Windows, Mac or Linux) and follow a few very simple examples that will give you a taste of the syntax and power of R, data handling, plotting, etc. Can you spot the errors (3) in the tutorial?
At the time of this writing, these are R-version 3.02 and RStudio version v0.97.551.

In case you want to go further, installing the basic DESeq package is a matter of typing 3 lines in your console:

• source("http://bioconductor.org/biocLite.R")
• biocLite("BiocUpgrade")
• biocLite("DESeq")

the next 2 lines will start the package and open a pdf with the DESeq-tutorial:

• library(DESeq)
• vignette("DESeq")

These packages will come pre-installed during the course, so you don't need to do this yourself now.

You can find a print-ready course announcement here

day 1 - Wednesday, June 5th, 2013

day 2 - Thursday, June 6th, 2013

day 3 - Friday, June 7th, 2013