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Fri 15 Mar, Mon 18 Mar, Tue 19 Mar 2024
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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Fri 21 Jun 2024


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Analysis of bulk RNA-seq data (IN-PERSON)
Prerequisites

Fri 15 Mar, Mon 18 Mar, Tue 19 Mar 2024

Description

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.


If you do not have a University of Cambridge Raven account please book or register your interest here.

Additional information
  • ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
  • Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
  • Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
  • Further details regarding eligibility criteria are available here.
  • Guidance on visiting Cambridge and finding accommodation is available here.
Target audience
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
Prerequisites
  • Required: Basic familiarity with the Unix command line and the R scripting language.

Please make sure to attend The Introduction to working with UNIX and bash course and/or having a working knowledge of the UNIX command line and the Introduction to R for biologists course and/or having a working knowledge of R.

If you are not able to attend a Unix and R course beforehand or want a refresher, at minimum please review the following material: Basic Command Line and Introduction to R for biologists.

Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Fri 15 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ian Tsang ,  Chandra Chilamakuri,  Ashley Sawle,  Dr P. Sardar
2 Mon 18 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ian Tsang ,  Chandra Chilamakuri,  Ashley Sawle,  Dr P. Sardar
3 Tue 19 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building map Ian Tsang ,  Chandra Chilamakuri,  Ashley Sawle,  Dr P. Sardar
Topics covered

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

Objectives

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
Aims

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
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics
Session 1 Introduction to RNA-seq methods
Session 2 Raw read file format and QC
Session 3 Quantification of Gene Expression with Salmon
Session 4 QC of alignment
Session 5 Exploratory Analysis of RNA-seq data
Day 2 Topics
Session 1 Introduction to RNA-seq Analysis in R
Session 2 Statistical Analysis of bulk RNA-seq data
Session 3 Differential Expression for RNA-seq
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
  • £ 60/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.
  • £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 120/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

3

Frequency

Several times per year

Related courses
Theme
Bioinformatics

Booking / availability