See the foot of the page for general information such as pricing and how to book.

Command Line Bioinformatics and High-throughput Sequencing Analysis

April 4th - 6th 2017

This course is supported by a BBSRC Strategic Training Award for Research Skills. It is therefore offered free of charge to Newcastle University and BBSRC-funded researchers.

Many powerful bioinformatics applications do not come packaged with an easy-to-use graphical user interface. Since many people are unfamiliar and uncomfortable with the command-line interface that is necessary to get such applications to work, they are unable to unlock the full potential of the valuable data they are generating. The aim of this course is to enable scientists with no prior exposure to a command-line interface to get up and running with this kind of work, and provide them with the fundamentals to use any command-line application. We will start from the basics (not assuming any prior knowledge), and will move through popular bioinformatics tools such as BLAST. The second and third days of the course will focus on tools for the analysis of high-throughput (or “next generation”) sequencing data.

Course Schedule

Day 1

  • Linux Basics
    • What is Linux?
    • What is it good for?
    • An introduction to `ls`, `cp`, `man`, `grep`, and many other tools that we’ll build upon throughout the rest of the course
  • Multiple Sequence Alignments

Day 2

  • Introduction to sequencing technologies
  • Common file formats
    • FASTQ
    • SAM & BAM
    • BED
  • Quality Control
  • De novo High Throughput Sequence Assembly
  • High Throughput Sequence Alignment (mapping to a reference genome)

Day 3

  • Tools for RNA-Seq Analysis
  • Batch processing with High-Performance Computing


May 16th - 20th 2016

Course outline:

This is a five day intensive course on R and Bioconductor. The course will be a mixture of lectures and computer practicals. The final day provides participants an opportunity to analyse their own data.

No prior programming knowledge of any kind is assumed.

Course structure:

This course will be structured as follows:

  • Day 1: Introduction to R
    • Standard R data types
    • Manipulating data
    • Base graphics
  • Day 2: Bioconductor input/output
    • Object oriented programming in R
    • What is Bioconductor?
    • Installing packages
    • Loading Affymetrix and Illumina data into R
  • Day 3: Finding differentially expressed genes
    • Data quality checks
    • Microarray data analysis with Limma
  • Day 4: Functional Analysis and Data Integration
    • Clustering
    • GO stats
    • Biomart
  • Day 5: RNA-Seq and Analysis of participants’ data
    • Introduction to RNA-Seq
    • Analysis with DESeq2 and Limma Voom


  • Dr Colin Gillespie, Statistics Lecturer in the School of Mathematics & Statistics.
  • Dr Simon Cockell, Newcastle Bioinformatics Support Unit
  • John Casement, Newcastle Bioinformatics Support Unit


Spaces can be reserved for the High Throughput Sequence Analysis course by clicking on the links in the table below, spaces on all other courses and for external people can be reserved by emailing Simon Cockell. The Bioconductor course is booked via the school of Mathematics and Statistics.  All courses are subject to a fee.

Booking links (Cost)
Course Length Newcastle University External - Academic/NHS/Charity External - Commercial
High Throughput Sequence Analysis
3 days (4th - 6th April 2017) FREE
Book Here
Book Here
Book Here
Bioconductor 5 days Book (£520) Book (£600) Book (£800)


Command Line

The Command Line course is free for Newcastle University staff and students, and BBSRC-funded researchers. However, in the event of a cancellation less than one week from the start of the course, a £100 fee will be charged.

For all other participants, a cancellation up to one week before the course start date will incur a 30 per cent cancellation fee. For later cancellations, or non attendance, the full course fee will be charged.


Cancellations up to 14 days before the course start date will incur a 30 per cent cancellation fee. For later cancellations, or non attendance, the full course fee will be charged.