RNA-Seq Next Generation Sequencing Analysis Workshop October 2016


Venue: University of Leicester - College Court Conference Centre
Date: 26th, 27th, 28th October 2016
Time: 9:00am to 5:00pm each day
Organizers: Matt Blades, Chiara Batini and Ben Hunt
Admin support: Matt Blades & Chiara Batini - bbash2016@le.ac.uk
Registration:  CLOSED
Participation:  Open application with selection


Course Overview

This course will provide an introduction to next generation sequencing (NGS) platforms, data analysis and tools for data quality control, read alignment (mapping), differential expression, denovo and referenced based transcriptome assembly, annotation and gene discovery of RNA sequencing (RNA-Seq) data.  The course will be delivered using a mixture of lectures and computer based hands on practical sessions using real data.



This course is aimed at wet-lab biologists who are involved in research projects that will require the handling and analysis of NGS data.

A significant proportion of the course will be computer-based using command line tools in the Unix environment, therefore, in order to gain maximum benefit from the course all attendees will be required to have basic Unix skills. This means applicants must at a minimum be able to move easily around the file system and make directories (e.g. pwd, cd, ls, mkdir), manage files (e.g. cp, mv, ln, rm, less, head, tail, wc) and search with grep.

IT services will be running an ‘Introduction to Linux’ course in the week commencing 17th October (date to be confirmed) specifically for University of Leicester attendees of this RNA-Seq workshop.  If you are selected to attend the workshop and are not an experienced Unix user, then a place will be reserved for you on the 'Introduction to Linux' course.


Registration is now CLOSED.

The course application process closed on Friday 30th September 2016.


During this course you will learn about:

•    The commonly used NGS platforms and data output files.
•    Quality control and filtering of raw RNA-Seq read data
•    Mapping of reads to reference genome and differential expression analysis
•    De-novo transcriptome assembly, assessment of assembly quality, annotation and gene discovery


Day 1 Overview: Introduction to NGS platforms, unix recap, data formats and quality control

A range of different platforms are available for NGS, these will be described and the key advantages/disadvantages discussed.  The commonly used output data file formats and workflows will be discussed along with a practical session illustrating a workflow for quality control and filtering of raw RNA-Seq read data.

Learning objectives:

•    Develop an understanding of NGS platforms
•    Introduction to workflows
•    NGS data formats
•    QC and pre-processing of raw data (FastQC, Trimmomatic)



Day 2 Overview – Mapping to a reference, differential expression analysis & de-novo transcriptome assembly

Day 2 will consist of an introduction to mapping RNA-Seq reads to a reference genome and highlighting some of the issues compared to aligning DNA-Seq reads.  Differential expression analysis will also be covered, followed by hands-on sessions to put the theory into practice.  De-novo transcriptome assembly will also be introduced in preparation for day 3.

Learning objectives:

•    Develop an understanding of read mapping and de-novo assembly strategies
•    Mapping reads to a reference genome using TopHat/STAR
•    Differential expression analysis using cufflinks and cummeRbund
•    De-novo transcriptome assembly using Trinity/Trans-ABySS/Bridger



Day 3 Overview – De-novo assembly assessment and annotation

This day will continue to focus on de-novo transcriptome assembly and the subsequent steps involved in differential expression analysis.  Transcriptome assembly assessment will then be investigated along with methods for assembly annotation and gene discovery, followed by practical sessions.

Learning objectives:

•    Develop an understanding of methods for de-novo transcriptome assembly, assembly assessment and annotation
where no reference genome exists
•    De-novo transcriptome assembly using Trinity/Trans-ABySS/Bridger
•    Differential expression analysis using RSEM and edgeR
•    Assembly assessment, annotation and gene discovery using Transrate, transdecoder, BLAST+ and CDHIT




RNA-Seq October 2016 workshop timetable

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