CRUK Bioinformatics Summer School 2021: Functional Genomics
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21st - 27th July 2021: Zoom virtual school, University of Cambridge
Site short-cut: https://tinyurl.com/crukss2021
Overview
Functional genomics looks at the dynamic aspects of how the genome functions within cells, particularly in the form of gene expression (transcription) and gene regulation. This workshop surveys current methods for functional genomics using high-throughput technologies.
High-throughput technologies such as next generation sequencing (NGS) can routinely produce massive amounts of data. However, such datasets pose new challenges in the way the data have to be analyzed, annotated and interpreted which are not trivial and are daunting to the wet-lab biologist. This course covers state-of-the-art and best-practice tools for bulk RNA-seq and ChIP-seq data analysis, and will also introduce approaches in prognostic gene signatures.
Audience
Enthusiastic and motivated wet-lab biologists who want to gain more of an understanding of NGS data and eventually progress to analysing their own data
Pre-requisites
The course will include a great deal of hands-on work in R and at the command line. In order for you to make the most of the course we strongly recommend that you take an introductory course, or have sufficient experience in the following areas:
- R
- Unix
- Introductory statistics
More specific requirements and references can be found here
Instructors & helpers
- Rory Stark (CRUK CI).
- Shamith Samarajiwa (MRC CU)
- Izzy Newsham (MRC CU).
- Junfan Huang (MRC CU).
- Ashley Sawle (CRUK CI).
- Abigail Edwards (CRUK CI).
- Jon Price (Gurdon Institute, Cambridge).
- Kamal Kishore (CRUK CI).
- Stephane Ballereau (CRUK CI).
- Zeynep Kalender Atak(CRUK CI).
- Chandra Sekhar Reddy Chilamakuri (CRUK CI).
- Hugo Tavares (Bioinformatics Training Facility, Dept of Genetics, CU)
- Katarzyna Kania (CRUK CI).
- Mark Fernandes (CRUK CI).
- Matthew Eldridge (CRUK CI).
Support Team
Craik-Marshall team.
- Alexia Cordona.
- Cathy Hemmings.
- Paul Judge.
CRUK Cambridge Centre. - Birgitta Olofsson.
- Justin Holt.
Aims
During this course you will learn about:-
- How aligned sequencing reads, genome sequences and genomic regions are represented in R.
- How to handle NGS data and read sequencing data with R, perform quality assessment and execute standard pipelines for (bulk) RNA-Seq and ChIP-Seq analysis
- How to do downstream analysis of transcription factor (TF) and epigenomic (histone mark) ChIP-seq data.
Objectives
After the course you should be able to:-
- Know what tools are available in Bioconductor for HTS analysis and understand the basic object-types that are utilised.
- Process and quality control short read sequencing data
- Given a set of gene identifiers, find out whereabouts in the genome they are located, and vice-versa
- Produce a list of differentially expressed genes from an RNA-Seq experiment.
- Import a set of ChIP-Seq peaks and investigate their biological context.
Day 0 (July 20th )
**SOCIAL 18:00 - .. Informal get-together on Zoom with optional pub-quiz. Meet fellow attendees and some of your trainers.
School Shared document is here **
Day 1 (July 21st)
Zoom Virtual Training room.
July 221st - 27th 2021
- 09:00 - 09:40; Welcome (Paul & Mark) & What is Functional Genomics? (Rory)
- 09:40 - 12:30; Data Processing for Next Generation Sequencing (Shamith, Izzy & Junfan)
- Lecture 1: Introduction to next generation sequencing
- Lecture 2: Quality control and trimming
- Practical 1: QC and quality trimming of raw sequencing reads
- Lecture 3: Short read alignment and Quality Control
- Practical 2: Short read alignment with STAR
- Practical 2 Solutions
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12:30 - 13:30; LUNCH BREAK
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13:30 - 17:00; Bulk RNAseq
- 13:30 - 14:00 Introduction to RNAseq Methods (pdf) - Ashley Sawle
- 14:00 - 15:00 Quantification of Gene Expression with Salmon (pdf) - Ashley Sawle
- 15:00 - 17:00 - RNA-seq Data Exploration (pdf) - Ashley Sawle
- Extended Material
Day 2 (July 22nd) - Bulk RNAseq
- 09:30 - 13:00 Statistical Analysis of Bulk RNAseq Data
- Part I: Statistics of RNA-seq analysis - Zeynep Kalender Atak
- Part II: Linear Models in R and DESeq2 (pdf) - Hugo Tavares
- Slides
- Find the worksheet in
Course_Materials/RNAseq/stats/models_in_r_worksheet.R
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13:00 - 14:00; LUNCH BREAK
- 14:00 - 17:00 Differential Expression for RNA-seq (pdf) - Ashley Sawle
Day 3 (July 23rd)
- 09:30 - 12:30; Bulk RNAseq
- 09:30 - 11:15 Annotation and Visualisation of RNA-seq results (pdf) - Abbi Edwards
- 11:15 - 12:30 Gene-set testing - Stephane Ballereau
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12:30 - 13:30; LUNCH
- 13:30 - 17:00; Single Cell RNAseq
- 13:30 - 14:15 Introduction
- Slides - Katarzyna Kania
- 14:15 - 14:30 Preamble: data set and workflow - Stephane Ballereau
- 14:30 - 15:55 Library structure, cellranger for alignment and cell calling, preprocessing - Ashley Sawle
- 15:55 - 16:05 10 min break
- 16:05 - 17:30 Normalisation - Stephane Ballereau
**6pm SOCIAL: Zoom Talk: “Perspectives on AI by Rory Stark”. **
Weekend - recharge your batteries!
SOCIAL: Punting tour of Cambridge
SOCIAL: Virtual tour of Cambridge University Botanical Gardens
SOCIAL/WORK: Virtual tour of CRUK Cambridge Institute
SOCIAL: Aeriel 360 panoramas of Cambridge venues
WORK: For those who feel the need to brush up on their linux skills
WORK: For those wanting an R course with extensive use of Tidyverse
Day 4 (July 26th) Single Cell RNAseq continued
- 09:30 - 10:55 Dimensionality reduction, feature selection - Zeynep Kalender Atak
- 10:55 - 11:05 10 min break
- 11:05 - 12:30 Batch correction and data set integration - Abigail Edwards
- Slides
- Data set integration
Extended Materials - Batch correction
- 12:30 - 13:30 LUNCH
- 13:30 - 14:30 Clustering - Stephane Ballereau
- 14:30 - 15:25 Cluster marker genes - Zeynep Kalender Atak
- 15:25 - 15:35 10 min break
- 15:35 - 16:30 Differential expression and abundance between conditions - Stephane Ballereau
- 16:30 - 17:30 Trajectories - Zeynep Kalender Atak
Day 5 (July 27th)
- 09:30 - 17:00;
- ChIP-seq data analysis (Shamith, Izzy & Junfan)
- Lecture 1: Introduction to ChIP-seq
- Lecture 2: Introduction to Peak Calling
- Practical 1: Peak calling with MACS2
- Lecture 3: Quality control methods for ChIP-seq
- Practical 2: QC & Integrative Genome Viewer
- Lecture 4: Downstream analysis of ChIP-seq
- Practical 3: Downstream analysis of ChIP-seq
- 12:30 - 13:30; LUNCH BREAK
Course Feedback.
Please don’t forget to fill in the survey