This course will familiarise participants with advanced data analysis methodologies in the field of transcriptomics and to provide practical training in the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from RNA-Seq experiments and illustrate different ways of analysing the generated data. Practicals will enable participants to apply statistical methods to the analysis of RNA-Seq data under the guidance of the trainers.

Who is this course for?

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor.

What will I learn?

Learning outcomes

After this course you should be able to:

• Understand the advantages and limitations of the high-throughput assays presented
• Assess the quality of your datasets
• Understand the difference between short read aligners
• Perform alignment and quantification of expression of RNA-seq datasets
• Understand the challenges of single cell sequencing analysis

Course content

During this course you will learn about:

• High-throughput sequencing technology
• Quality control of raw reads: FASTQC and fastx toolkit
• Considerations on experiment design for RNA-seq
• Read pseudoalignment and quantification: kallisto, salmon
• Differential expression analysis and differential exon usage: R, edgeR, DESeq2, DEXSeq
• Downstream DE data processing and gene target discovery
• Single cell RNA-seq analysis: scran, scater

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

1. Complete the online application form
2. Submit a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Frank O'Donnell (frank@ebi.ac.uk) by 12:00 GMT on Friday 11 January, 2019.

Incomplete applications will not be considered.

Participants have the opportunity to display an A2 (420x594mm - portrait) poster for the duration of the course. We will ask you to submit your poster before the course for printing on site. It is not possible to display posters of a different size or orientation.

Accommodated will be provided at the Holiday Inn, Impington Monday-Friday inclusive. This location is difficult to access from both the Wellcome Genome Campus or Cambridge and we strongly recommend that successful participants consider finding alternative accommodation close to Cambridge Station prior to or after the course to ease journeys. Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates.

The course includes evening meals at the Hinxton Hall Restaurant on campus, and breaks and lunches outside the EMBL-EBI training rooms.