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Mon 18 Jun - Wed 20 Jun 2018
09:30 - 17:30

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

Provided by: Bioinformatics


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Fri 17 Mar 2023


Fri 23 Jun 2023


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Introduction to RNA-seq data analysis
Updated

Mon 18 Jun - Wed 20 Jun 2018

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.

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 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 one of the many UNIX tutorials available online.
  • 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 Mon 18 Jun 2018   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Luigi Grassi,  G.E. Parada-Gonzalez
2 Tue 19 Jun 2018   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr Luigi Grassi,  G.E. Parada-Gonzalez,  Oscar Rueda
3 Wed 20 Jun 2018   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Ashley Sawle,  Dr S. Ballereau
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 Speaker(s)
09:30 - 10:30 Lecture: Introduction to RNA-seq Luigi Grassi, Guillermo Parada Gonzalez
10:30 - 10:45 Tea/coffee break
10:45 - 12:00 Practical: RNA-seq analysis - qc and adapter removal Luigi Grassi, Guillermo Parada Gonzalez
12:00 - 13:00 Lunch (not provided)
13:00 - 15:00 Practical: RNA-seq analysis - alignment and transcriptome reconstruction Luigi Grassi, Guillermo Parada Gonzalez
15:00 - 15:15 Tea/coffee break
15:15 - 17:30 Practical: RNA-seq analysis - transcriptome merging, comparison and quantification Luigi Grassi, Guillermo Parada Gonzalez
Day 2
09:30 - 10:00 Practical: RNA-seq analysis - Alignment and quantification with STAR Luigi Grassi, Guillermo Parada Gonzalez
10:00 - 10:15 Tea/coffee break
10:15 - 12:00 Practical: RNA-seq analysis - Salmon quasi-alignment Luigi Grassi, Guillermo Parada Gonzalez
12:00 - 13:00 Lunch (not provided)
13:00 - 15:00 Lecture/practical: Linear Models and Statistics for Differential Expression Oscar Rueda
15:00 - 15:15 Tea/coffee break
15:15 - 17:30 Lecture/practical: Linear Models and Statistics for Differential Expression Oscar Rueda
Day 3
09:30 - 11:00 Importing and Preprocessing in R Ashley Sawle
11:00 - 11:15 Tea/coffee break
11:15 - 12:30 Differential Expression Ashley Sawle
12:30 - 13:30 Lunch (not provided)
13:30 - 15:00 Annotation and Visualisation of Differential Expression Stephane Ballereau
15:00 - 15:15 Tea/coffee break
15:15 - 17:00 Gene set analysis and Gene Ontology testing Stephane Ballereau
Registration fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, 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
Specialised Training

Booking / availability