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Wed 30 Jun - Fri 2 Jul 2021
09:30 - 17:30

Venue: Bioinformatics Training Facility - Online LIVE Training

Provided by: Bioinformatics


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Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING)

Wed 30 Jun - Fri 2 Jul 2021


PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data.

This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

Number of sessions: 3

# Date Time Venue Trainers
1 Wed 30 Jun 2021   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Zeynep Kalender-Atak,  Jon Price,  Abigail Edwards
2 Thu 1 Jul 2021   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Abigail Edwards,  Ashley Sawle,  Hugo Tavares
3 Fri 2 Jul 2021   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Dr S. Ballereau,  Abigail Edwards,  Chandra Chilamakuri
Topics covered

Bioinformatics, Functional genomics, Data visualisation, Transcriptomics, Data handing, Data mining, RNA-seq


After this course you should be able to:

  • Design properly your RNA-Seq experiments considering advantages and limitations of RNA-seq assays
  • Assess the quality of your datasets
  • Perform alignment and quantification of expression through different tools and pipelines
  • Know what tools are available in Bioconductor for RNA-seq data analysis and understand the basic object-types that are utilised
  • Produce a list of differentially expressed genes from an RNA-seq experiment

During this course you will learn about:

  • RNA sequencing technology and considerations on experimental design
  • Quality control of raw and aligned sequencing reads: FASTQC and Picard
  • Read alignment to a reference genome: Hisat2
  • Extract information from SAM/BAM files: samtools
  • Sources of variation in RNA-seq data
  • Differential expression analysis usingDEseq
  • Annotation resources in Bioconductor
  • Identifying over-represented gene sets among a list of differentially expressed genes

Presentations, demonstrations and practicals


This is subject to change in line with the online training schedule.

Day 1 Topics
Session 1 Introduction to RNA-seq Methods
Session 2 Raw read file format and QC
Session 3 Short read alignment with HISAT2
Lunch (not provided)
Session 4 QC of alignment
Session 5 Quantification of Gene Expression with Salmon
Day 2 Topics
Session 1 Introduction to RNAseq Analysis in R
Session 2 RNA-seq Pre-processing
Lunch (not provided)
Session 3 Statistical Analysis of Bulk RNAseq Data
Session 4 Experimental Design of Bulk RNAseq studies
Day 3
Session 1 Differential Expression for RNA-seq
Lunch (not provided)
Session 2 Annotation and Visualisation of RNA-seq results
Session 3 Gene-set testing
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here



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