Courses@CRG: RNA-Seq Library preparation and data analysis

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08/06/2020 12/06/2020

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Courses@CRG: RNA-Seq Library preparation and data analysis

Description of the course

The “Courses@CRG: RNA-Seq library preparation and data analysis” will provide an introduction to the RNA sequencing and library preparation technologies and data analysis tools and resources. This course will focus on the preparation of next generation sequencing RNA-seq library for the Illumina HiSeq platform followed by data analysis and interpretation of the results. The content is intended to provide a broad overview on the most advanced RNA library preparation techniques and applications and to introduce participants to computational data analysis using command line programs and the R programming language. It will also highlight key resources, approaches and methodologies to start with the analysis of transcriptomics data and to provide biological interpretation of the results. The course combines lectures with practical hands-on sessions in the laboratory and bioinformatics training room to consolidate the concepts introduced during the theoretical sessions. An important part of the course will concern the definition of a good experimental design, quality control steps and troubleshooting. For the library preparation, participants will have an opportunity to bring up to two samples. The course will be taught by experienced instructors from the CRG core facilities who use these protocols on a daily basis.

Main goals

At the end of the course, the participants will be able to:

Prepare RNA libraries with TruSeq stranded mRNA protocol
Perform quality control of libraries
Get an overview of state of the art of RNA sequencing
Define a proper experimental design including sequencing design, and quality control steps
Perform quality assessment of RNA-seq data and results
Understand file formats commonly used in RNA-seq data analysis
Gain an overview of some of the common software tools for RNA-seq data analysis and their limitations
Being able to mine and retrieve gene expression data from public repositories
Understand the analysis steps from raw reads to differential expression analysis and interpretation of the results

Duration

5 days: Course will start on Monday 8th of June 2020 at 9am and finish on Friday 12th June 2020 at 6 pm.

Organizers and instructors

CRG Genomics and Bioinformatics core facilities:

	Jochen Hecht		Julia Ponomarenko
	Magda Monfort		Luca Cozzuto
	Marta Forn		Sarah Bonnin
	Núria Andreu		Toni Hermoso

Target audience and number of participants

The course targets international postdocs, PhD students and technicians from the molecular biology or clinical fields, as well as researchers in industry whose projects involve use of RNA libraries preparation and transcriptomic analysis.

Number of participants: 16

Participants are required to have a basic knowledge of the Linux command line and the of R language.

We recommend these free tutorials that can be used to practice basics in Linux and R before coming to the course.

Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
Linux: https://biocorecrg.github.io/advanced_linux_2019/
Introduction to R: https://biocorecrg.github.io/CRG_RIntroduction/

Registration

Application deadline: 31st March 2020

Chosen participants will be notified by: Worldwide participants will be selected according to their CV and motivation statement. Selected participants will be notified via email by early April 2020.

Registration fee: 400€ (+21% VAT) for academic researchers, 500€ (+21% VAT) for industry. Inscription fees includes participation in workshop, lab reagents, all the necessary tools to follow the course, didactic material, protocols, coffee breaks, lunches, networking event.

Only on-line application accepted - Registration HERE