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Wed 27 Mar - Fri 29 Mar 2019
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Wed 25 Mar 2020


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Introduction to RNA-seq data analysis
Updated

Wed 27 Mar - Fri 29 Mar 2019

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.

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.
  • Further details regarding eligibility criteria are available here
Prerequisites
  • Basic experience of command line UNIX
  • Sufficient UNIX experience might be obtained from Tutorials 1-4 of this UNIX tutorial.
  • Basic knowledge of the R syntax
  • For a real beginner's introduction into R see here. More advanced R instructions can be found at Quick-R or An Introduction to R
Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Wed 27 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map G.E. Parada-Gonzalez,  Ashley Sawle
2 Thu 28 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map G.E. Parada-Gonzalez,  Dominique-Laurent Couturier,  Dr A. Edwards
3 Fri 29 Mar   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr S. Ballereau,  Ashley Sawle,  Dominique-Laurent Couturier,  Dr A. Edwards
Topics covered

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

Objectives

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
Aims

During this course you will learn about:

  • RNA sequencing technology and considerations on experiment design
  • Quality control of raw sequencing reads: FASTQC and fastx toolkit
  • Read alignment to a reference genome: Hisat2
  • Extract information from SAM/BAM files: samtools
  • Transcriptome reconstruction: stringtie
  • Transcriptome merging, comparison and quantification: gffcompare and stringtie
  • Genome alignment and read count quantification: STAR
  • Lightweight alignment and quantification: Salmon
  • Sources of variation in RNA-seq data
  • Differential expression analysis using edgeR and DEseq
  • 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
09:30 - 10:15 Lecture: Introduction to RNA-seq Methods
10:15 - 10:45 Introduction to Alignment and Quantification
10:45 - 12:30 Practical: Basic Unix, input file formats and quality control
12:30 - 13:30 Lunch (not provided)
13:30 - 16:00 Practical: Mapping reads to the genome and getting raw counts
16:00 - 17:30 Practical: Introduction to reproducible bioinformatics
Day 2
09:30 - 10:00 Practical: Connecting snakemake workflows
10:00 - 11:15 Practical: Guided transcriptome assembly using StringTie
11:15 - 12:30 Practical: Alternative splicing analysis using Whippet
12:30 - 13:30 Lunch (not provided)
13:30 - 14:00 Introduction to RNAseq Analysis in R
14:00 - 14:45 RNA-seq Pre-processing
14:45 - 17:30 Linear Model and Statistics for Differential Expression
Day 3
09:30 - 12:00 Differential Expression for RNA-seq
12:00 - 13:00 Lunch (not provided)
13:00 - 15:30 Annotation and Visualisation of RNA-seq results
15:30 - 17:30 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
Duration

3

Frequency

2 times a year

Related courses
Theme
Specialized Training

Booking / availability