ChIP-seq data analysis, 1 hp

National course open for PhD students, postdocs, researchers and other employees in need of ChIP-seq data analyses skills within all Swedish universities.

The course is organized by NBIS

Responsible teachers: Olga Dethlefsen, Agata Smialowska


This course provides a practical introduction to analyzing ChIP-seq data. It is aimed for those already working with NGS data analyses but in need of learning best practice bioinformatics methods for processing and analyses of ChIP-seq data. Upon completion of the course, attentive participants will be able to plan and run most common ChIP-seq data analyses.

Important dates

Application open: 2017-08-28

Application page

Application deadline: 2017-10-06

Acceptance confirmation: 2017-10-16

If you do not receive information according to the above dates please contact:

Course content

This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data including:

  • Quality controls of raw sequencing reads
  • Reads trimming and filtering
  • Alignment to the reference genome
  • Peak-independent quality metrics
  • Peak calling
  • Peak-dependent quality metrics and visualization
  • Differential binding analysis
  • Functional analysis, incl. finding nearest genes, exons and custom features, obtaining enriched Gene Ontology terms and pathways

Entry requirements

Required for being able to follow the course and to complete computer exercises:

  • At least basic knowledge in Linux
  • Ability to bring your own laptop with R installed for the computer exercises
  • Programming / scripting experience, preferably in R


  • Experience working on Uppmax or another HPC
  • Previous experience with NGS data analyses
  • Completing SciLifeLab / NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists”

Selection criteria

The course can accommodate 15 participants. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Course fee

1300 SEK (includes lunches, coffee and snacks)

*Please note that SciLifeLab cannot invoice individuals