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Fri 17 Mar, Mon 20 Mar, Tue 21 Mar 2023
09:30 - 17:30

Venue: Bioinformatics Training Room

Provided by: Bioinformatics


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Analysis of bulk RNA-seq data (IN PERSON)

Fri 17 Mar, Mon 20 Mar, Tue 21 Mar 2023


PLEASE BE AWARE: This event is run in-person, if you wish to book for the online version, please click here.

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.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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.
  • After you have booked a place, if you are unable to attend any of the live sessions and would like to work in your own time, please email the Bioinfo Team as Attendance will be taken on all courses. A charge is applied for non-attendance, including for registered university students.
  • Further details regarding eligibility criteria are available here

Number of sessions: 3

# Date Time Venue Trainers
1 Fri 17 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room map Hugo Tavares,  Ashley Sawle,  Dr A. Edwards,  Jiayin Hong,  Sina Beier
2 Mon 20 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room map Ashley Sawle,  Dr A. Edwards,  Jiayin Hong,  Jon Price
3 Tue 21 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room map Ashley Sawle,  Dr A. Edwards,  Sina Beier
Topics covered

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


After this course you should be able to:

  • Design your RNA-Seq experiments properly, 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


Day 1 Topics
Session 1 Introduction to RNA-seq methods
Session 2 Quality control of raw sequencing data
Session 3 Alignment and quantification of gene expression
Session 4 Alignment quality control
Session 5 Exploratory analysis of RNA-seq data
Day 2 Topics
Session 1 Statistical analysis of bulk RNA-seq data
Session 2 Differential expression analysis
Day 3 Topics
Session 1 Annotation and Visualisation of RNA-seq results
Session 2 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



Several times per year

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