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RNA-seq, 1 hp

National course open for PhD students (prioritized), postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application form

Important dates

Application open: October 28, 2016

Application deadline: February 6, 2017

Confirmation to accepted students: February 13, 2017

Responsible teachers: Johan Reimegård

If you don’t receive information according to the dates above, contact

Course fee

A course fee of 1300 SEK will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

Course website

This course will cover both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq and biostatistics will cover a range of cutting-edge issues in RNA quality control, transcript assembly in model and non-model organisms, differential expression analysis and downstream analysis using other types of data. An extensive case study in the computer lab will familiarize you with concepts of mapping, quality control of your RNA-seq data, de novo assembly, assembly using a reference, differential expression analysis and downstream enrichment analysis.

Topics covered will include:

  • Gene and isoform detection using short RNA-seq reads
  • Gene and isoform detection using long RNA-seq reads
  • Gene and isoform detection combining RNA-seq data with other data sources
  • Quality assessment of RNA-seq data
  • Differential expression analysis using RNA-seq data on multiple cells
  • Downstream analysis after identifying differentially expressed genes.

Entry requirements

  • Basic knowledge in linux is a requirement! We will not teach Linux at the course and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment.
  • Be able to bring your own laptop for the practical computational exercises. If you don’t have a laptop to bring please contact before you register.
  • Some programming/scripting experience is desirable, but not required.
  • Experience working on the SNIC center Uppmax is desirable, but not required.
  • Participants of the SciLifeLab Course “Introduction to Bioinformatics using NGS data” (or alike) are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics.

Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.