RNA-Seq Analysis
This course
provides an introduction to the QC, processing and analysis of RNA-Seq data. It
focuses on a workflow where RNA-Seq is performed on a large eukaryotic genome
for which there is a reference genome available. The course starts with a
comprehensive lecture covering the theory of RNA-Seq data generation and
analysis and is then followed by hands-on practical sessions which run though
the entire RNA-Seq analysis pipeline from raw fastq files to a list of
differentially expressed candidate genes.
Quality Control in Sequencing Experiments
This course
looks at the different ways in which sequencing based studies can fail and the
options for visualisation and QC which allow you to identify and diagnose these
failures at an early stage. It is designed to be of use to anyone who is using
sequencing as part of their research, not just those who are running sequencing
facilities.
ChIP-Seq Analysis
This course
provides a complete introduction to the theory and practice of the analysis of
ChIP-Seq data. It is designed for biologists who may have limited practical
bioinformatics skills, but who would like to use ChIP-Seq as part of their
work. By the end of the course students should be able to process and analyse
their own data.
Students on
this course would benefit from having attended the SeqMonk or Unix introduction
courses, but these are not required in order to attend.
Analysing Mapped Sequence Data with SeqMonk
SeqMonk is a program which can analyse large data
sets of mapped genomic positions. It is most commonly used to work with data
coming from high-throughput sequencing pipelines.
The program
allows you to view your reads against an annotated genome and to quantitate and
filter your data to let you identify regions of interest. It is a friendly way
to explore and analyse very large datasets.
This course
provides an introduction to the main features of SeqMonk and will run through
the analysis of a couple of different datasets to show what sort of analysis
options it provides.
Analysing bisulfite methylation sequencing data
This course
builds on the core skills introduced in the Introduction to R, Introduction to
Unix and Introduction to SeqMonk courses to provide a more in depth look at the
analysis of bisulfite sequencing data. The course is a mix of theoretical
lectures and hands-on practicals which go through the whole analysis pipeline,
starting from raw sequence data and covering QC, visualisation, quantitation
and differential methylation analysis.
10X Single Cell RNA-Seq Analysis
This course
gives a practical introduction to the processing, qc and analysis of a simple
single cell RNA-Seq experiment performed on the 10X platform. It explains the
technology used to create the data and goes through some common analysis tools.
The course also goes through the theory and practice of the dimension reduction
techniques which are very often used to present this kind of data.