CRUK Bioinformatics Summer School 2019: Functional Genomics

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15th - 19th July 2019: Craik-Marshall Room, Downing Site, University of Cambridge

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

# (**Data files for course are here. There is a zip-file for each course and a sizes.txt file with zip sizes ** )

Instructors

• Mark Fernandes (CRUK CI).
• Rory Stark (CRUK CI)
• Shamith Samarajiwa (MRC CU).
• Dora Bihary (MRC CU).
• Joanna Krupka (MRC CU).
• Ashley Sawle (CRUK CI).
• Alistair Martin (CRUK CI).
• Stephane Ballereau (CRUK CI).
• Dominique-Laurent Couturier(CRUK CI).

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, ChIP-Seq and ATAC-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 or ATAC-seq peaks and investigate their biological context.

Day 0 (July 14th )

**SOCIAL 18:00 - .. Informal get-together at The Grain and Hop Store (close to accommodation in Downing College). Meet fellow attendees and some of your trainers.
Join us for a drink and dinner (self-paying), and to meet your colleagues for the next few days http://www.grainandhopstore-cambridge.co.uk/

**Note that the Training Room in Craik-Marshall building (1st Floor) will be open from 9am. School etherpad (E-whiteboard) is here **

Day 1 (July 15th)

Breakfast at Downing College is at 8.45-9.15am.

C-M Training room.

• 09:30 Course Introduction
• 09:30 - 10:30; Introduction to Functional Genomics
• 10:30 - 12:30; Introduction to Bioconductor.
• Bioconductor answers.
  • source
  • Source with solutions.
• 12:30 - 13:30; LUNCH
• 13:30 - 14:30 Principles of Experimental Design
• 14:30 - 17:00;
• Data processing for Next Generation Sequencing
  • Lecture 1: Introduction to next generation sequencing (2.30- 2.45pm)
  • Lecture 2: Brief introduction to file formats (2.45- 3.00pm)
  • Lecture 3: Quality control and artefact removal (3.00- 3.45pm)
  • Practical 1: learn to use FastQC and Cutadapt (20 min) on a sample dataset
  • Lecture 4: Short read alignment and Quality Control (3.45-5.00pm)
  • Practical 2: Alignment of a ChIP-seq dataset to a reference genome using BWA OR Bowtie2 and a RNA-seq dataset to STAR (45 min)

Day 2 (July 16th)

• 09:30 - 10:00;
  • Introduction to RNA-seq
• 10:00 - 11:30;
  • Counting
  • Importing and QC of RNA-seq data
    • Challenge Solutions
  • Supplementary Material: Obtaining raw reads from SRA
• 11:30 - 12:30 Linear models & differential expression
  • Slides
  • Annotated Slides
  • Linear models html nb
• 12:30 - 13:30; LUNCH
• 13.30 - 15:00; Linear models & differential expression (cont)
• 15:00 - 17:30
  • Differential expression analysis with DESeq2
    • Challenge Solutions

SOCIAL: Punting trip - leave from Mill Lane punting site at 18:00 (~10 min walk from Craik-Marshall) Google Map. Scudamore’s Web-site & Mill lane map.

Day 3 (July 17th)

• 09:30 - 11:00;
  • Annotation and Visualisation of Differential Expression
    • Challenge Solutions
  • Supplementary Material: Further visualistations
• 11:00 - 12:30;
  • Gene set analysis and Gene Ontology testing
    • Challenge Solutions
• 12:30 - 13:30; LUNCH
• 13:30 -14:00; Prognostic Gene Signatures (RS)
  • Slides

• 14:00 – 14:30; Survival Analysis (DL)
  + Slides
  + Annotated Slides
  + R Markdown doc.

• 14:30 – 15:00; Practical: Deriving a Predictive Gene Signature from DEGs
  • R Markdown doc.
• 15:00 – 15:30; Issues with prognostic gene signatures (RS)
  • Slides
• 15:30 – 16:00;
  Practical: Checking gene signatures with SigCheck
  • Practical

**SOCIAL: Summer School evening meal & Reception at the nearby Downing College at 18:30 to 22:30.. If you do not wish to attend this meal (free to attendees) then please let us know ASAP. Smart casual dress. http://www.dow.cam.ac.uk Downing College, Regent Street, Cambridge, CB2 1DQ (Site map in link below). The college should put up signage to help you find the venue.
The reception is at 6.30pm and dinner at 7.30pm Plus a post-Dinner talk: “Perspectives in AI for Cancer Bioinformatics by Rory Stark”. **
Drinks Reception 18:30- 19:30 Grace Howard Room, Dinner 19:30 -22:30 Grace Howard Room

Day 4 (July 18th)

• ChIP-seq data analysis
  • Lecture 1a: Introduction to ChIP-seq (9.30-9.45am)
  • Lecture 1b: Introduction to Peak Calling (9.45-10.30am)
  • Practical 1: Peak calling with MACS2 (10.30-11.00am)
  • Lecture 2: Differential binding analysis (11.00-11.30am)
  • Practical 2: THOR (and Diffbind) (11.30-12.00pm)
  • Lecture 3: Quality control methods for ChIP-seq (12.00-12.30pm)

  LUNCH (12.30-1.30pm)

  • Practical 3: Integrative Genome Viewer (1.30-2.00 min)
  • Lecture 4: Downstream analysis of ChIP-seq (2.00-2.30pm)
  • Practical 4: Downstream analysis of ChIP-seq (2.30-3.15pm)
  • Lecture 5: Introduction to (epi)Genomic data integration(3.15-3.45pm)
  • Practical 5: Data Integration for Genomics (TF direct targets & chromatin modifications) (3.45-5.00 min)

Day 5 (July 19th)

• 09:30 - 12:30; **A room in C-M building will be available for storing your baggage (There will be signage)
• Chromatin Accessibility
  • Lecture 1 Chromatin accessibility and nucleosome occupancy with ATAC-seq (9.30-10.00am)
  • Practical 1: ATAC-seq analysis (10.00-11.00am)
  • Lecture 2: Useful software utilities for the analysis of genomic data (11.00-11.30am)
  • Practical 2: Useful software utilities for the analysis of genomic data (11.30-12.30pm)
• 12:30 - 13:30; LUNCH
• Some of you may now be going to the CRUK Cambridge Centre Graduate Symposium Hope you enjoy it!
• Have a safe Journey home (Thank you for participating in the Summer School).
  

  Please don’t forget to fill in the survey