Bioinformatics Training at the CBRG

The Computational Biology Research Group run training courses in sequence analysis, ChiP-Seq analysis, RNA-Seq analysis and molecular biology software. The training courses are only available to CBRG full account holders unless stated otherwise (Note: holders of CBRG-proteomics accounts are not included).

Course Dates

Available Courses:

All courses are held in the Conference Room in the WIMM.

Course Dates:

Introduction to Bioinformatics

The course is not intended to be a comprehensive guide to all the bioinformatics packages available at the CBRG. Instead it is designed to show you the kind of analysis software that is available to you via your account. It should also ensure that you know where to look to find similar software on the CBRG web site and on the UNIX server to find help with any of the software on the system.

This course is intended for:

  • new users and/or anyone new to the WIMM
  • those that are not familiar with using their CBRG account for bioinformatics analysis

The course will be held in the Conference Room in the WIMM and is expected to last 2-3hrs. Each course is limited to 12 participants to allow for individual attention.


The course is designed in two parts:

Part one Introduction to some of the many bioinformatics analysis tools that are now available on this web site. The course will also introduce you to EMBOSS Explorer - a suite of bioinformatics software. You will be shown how to carry out some basic bioinformatics analyses - for example:

  • access the databases on our servers to retrieve sequence files
  • examine sequence file formats
  • run restriction analysis software
  • carry out sequence alignments and produce publishable images of the aligned sequences
  • search databases using BLAST & BLAT


Part two: Some of the bioinformatics tools are only available on our Unix servers and the second session will introduce the Unix computing facilities available via your molbiol account. We will cover:

  • how to connect to CBRG server using UNIX
  • an introduction to UNIX, using the command line
  • making directories, moving around, creating and viewing files, renaming files
  • editing text files using a basic text editor
  • using EMBOSS programs on the command line

Further UNIX

The course will introduce you to further useful UNIX commands which you will find helpful when using your CBRG account.

This course is intended for:

  • users that have just completed the Introduction course and want to learn more UNIX
  • those that already have a basic knowledge of UNIX.

The course will be held in the Conference Room in the WIMM and is expected to last 2-3hrs. Each course is limited to 12 participants to allow for individual attention.


The course will cover:

  • Piping
  • Output and input redirection
  • Wild cards and regular expressions
  • Custom tracks
  • Finding, sorting and looking at files
  • Configuring and managing your CBRG account
  • Quotas and disk usage
  • Modules



Introduction to UCSC Genome Browser

The course is an introduction to the UCSC Genome Browser (https://genome.ucsc.edu). It will lead you through the first steps of using UCSC Genome Browser, choosing genomes, moving around, adjusting and customising the browser display. It also covers loading custom tracks and making a sharing UCSC 'sessions'.

This course is intended for:

  • users that have never used the UCSC Genome browser
  • those that want to learn more about how to customise the displays and display their own data.

The course will be held in the Conference Room in the WIMM and is expected to last 2-3hrs. Each course is limited to 12 participants to allow for individual attention.


The course will cover:

  • Getting started with the UCSC Genome Browser
  • Adjusting the display
  • Finding genome locations
  • Custom tracks
  • UCSC sessions and sharing data
  • An introduction to track hubs



ChIP-Seq - This course has two parts, with an Introduction followed by a more advanced session usually one week later.

ChIP-Seq: Part I

Part I - This course is intended for users who are starting to analyse ChIP-Seq data. It will be held in the Conference Room in the WIMM and is expected to last 2-3hrs. Each course is limited to 12 participants to allow for individual attention.

The course will cover:

  • Downloading sequencing files from WTCHG
  • HTS data formats - fastq, SAM, BAM, BigWigs
  • Mapping HTS data using Bowtie
  • Creating and uploading BigWig file to UCSC Genome Browser
  • A look at SAMtools
  • Viewing BAM files at UCSC Genome Browser

The course is not intended to be a comprehensive guide to ChIp-Seq data analysis at the CBRG. Instead it is designed to show you the first steps - looking at your data or looking at data downloaded from GEO (a seperate tutorial on this is coming soon)

ChIP-Seq: Part II

Part II - This course is the second part of the ChIP-Seq analysis course and is intended to show how to peak call and view the results.
It will be held in the Conference Room in the WIMM and is expected to last 2-3hrs.
Each course is limited to 12 participants to allow for individual attention.


The course will cover:

  • Peak calling using MACS2
  • Annotating output files
  • Using MIG - Multi Image Genome Viewer to view the results.

RNA-Seq - This course has three parts, with an Introduction followed by two advanced sessions usually in consecutive weeks.

RNA-Seq: Part I

Part I - This course is intended for users who are starting to analyse RNA-Seq data. It will be held in the Conference Room in the WIMM and is expected to last 3hrs. Each course is limited to 12 participants to allow for individual attention.

The course includes a presentation on "An Introduction to Transcriptomics" by Steve Taylor - Head of CBRG, and will cover:

  • Downloading sequence files from WTCHG
  • HTS data formats - fastq, SAM, BAM, BigWigs
  • Mapping HTS data using STAR
  • Creating and uploading BigWig file to UCSC Genome Browser to view your data
  • A look at SAMtools
  • Counting Reads with featureCounts

The course is not intended to be a comprehensive guide to RNA-Seq data analysis at the CBRG. Instead it is designed to show you the first steps - looking at your data or data downloaded from GEO

RNA-Seq: Part II

Part II - This course is intended for users who want to analyse RNA-Seq data using bioconductor and edgeR and is a pre-requisite for the next part (Part III - Differential Gene Expression usin R and Bioconductor). It will be held in the Conference Room in the WIMM and is expected to last 3hrs. Each course is limited to 12 participants to allow for individual attention.

The course will cover:

  • Using Rstudio
  • Basic data: variables and vectors
  • Functions
  • R packages
  • Matrices, arrays, lists, data frames and factors
  • Indexing and conditional selection

The course is not intended to be a comprehensive guide to using R. Instead it is designed to show you the first steps in order for you to be able to use R packages to complete differential gene expression analysis in part III.

RNA-Seq: Part III

Part III - This course is intended for users who want to carry out differential gene expression analysis on RNA-Seq data. It will be held in the Conference Room in the WIMM and is expected to last 3hrs. Each course is limited to 12 participants to allow for individual attention.

The course will cover:

  • DGE analysis using Bioconductor tools and edgeR

The course is not intended to be a comprehensive guide to using Bioconductor and edgeR. Instead it is designed to show you how to complete differential gene expression analysis

Fiji

This course will be presented by Dominic Waithe, Optical Microscopy Image Analyst at the Wolfson Imaging Centre, WIMM

Details for this course will be added at a later date.

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