Epigenomics data analysis

National course open for PhD students, postdocs, researchers and other employees within all Swedish universities

Application closed

Important dates

Application closes: 2019-07-21

Confirmation to accepted students:  2019-08-01

Responsible teachers:  Agata Smialowska, Olga Dethlefsen

If you do not receive information according to the above dates please contact agata.smialowska@nbis.se, olga.dethlefsen@nbis.se

Course fee

A course fee* of 2000 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

Course content

This course builds on our previous ChIP-seq data analysis course to introduce the best practice bioinformatics methods for processing, analyses and integration of epigenomics data.

Topics covered:

  • ChIP-seq and ATAC-seq: peak calling, peak independent/dependent quality metrics, differential binding and differential accessibility analysis; motifs enrichment
  • Data processing and analyses for differential methylation with Illumina EPIC arrays and Bisulfite-seq
  • Functional analysis, incl. finding nearest genes and custom features, GO terms and Reactome pathways
  • Integrative visualisations of epigenomics datasets
  • RNA-seq integration for identification of direct transcriptional targets of transcription factors
  • Basic multi-omics exploration and integration

Entry requirements

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

  • BYOL, bring your own laptop with R and RStudio installed
  • Basic knowledge in Linux
  • Basic programming experience, preferably in R


  • Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run Uppmax tutorial before the course
  • Previous experience with NGS data analyses
  • Completing NBIS courses “Introduction to Bioinformatics using NGS data” and “R Programming Foundations for Life Scientists”

Due to limited space the course can accommodate maximum of 25 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.