The Bioinformatician’s Toolbox

Synopsis

Bioinformatic analysis is rapidly becoming a core skill for biologists. As an extremely varied field, there are a number of common fundamental approaches that can kick-start your research. Here we will explore a range, including interpreting and cleaning raw sequence data, genome assembly with short (illumina) and long (Nanopore/PacBio) data, RNAseq processing and analysis, and mapping to reference genomes (used for genome re-seq, CHipSeq, DNAseq/MNaseseq etc)

Objectives

This course provides the knowledge to process and understand the latest sequencing methodologies and technologies, and develop your own skills going forwards. Each topic is complex and nuanced (and could take a whole week course for each subject!) but here we will introduce a range of core skills which you can build upon.

We will always work with real biological data and industry standard bioinformatic tools to ensure that you can reproduce everything we do when you leave the course, and with all the background theory to understand exactly how the results are generated.

Instructor: Dr. Daniel Pass
Class size: 10-12 people
All days run 9:00-17:00 with 1h break

NOTE: The course will be run assuming attendees are comfortable navigating the linux command-line. If you don’t have this experience please consider the “Linux for Biologists” short course to prepare, which is half-price if booked together with this course.

Schedule

Day1

  • Introduction and course overview
  • Assessing raw NGS data – Is my data any good??
    Lunch
  • Manipulating and cleaning NGS Sequencing data
  • De novo Illumina short read genome assembly

Day2 

  • Writing loops for high throughput analysis
  • Using docker for software and reproducibility
    Lunch
  • Assessing genome assembly quality
  • Complex genome assembly with long read data (Nanopore/PacBio)

Day3

  • Genome annotation in simple (prokaryotic) and complex (higher eukaryotes)
    Lunch
  • Genome visualisation tools
  • Mapping to reference genomes

Day4

  • Mapping applications and interrogation – Brief context of Genome re-seq, ChIPSeq, DNase/MNase-seq etc
  • SNP calling
    Lunch
  • RNAseq transcriptome mapping, alignment and processing

Day 5

  • Differential Gene Expression with deseq2
  • Visualising DEG results – Heatmaps and NOT Venn diagrams!
    Lunch
  • Functional pathway analysis – Gene Ontologies and networks
  • Final summaries and your data Q&A
Book an upcoming course