ChIP-seq data analysis


National course open for PhD students, postdocs, researchers and other employees in need of ChIP-seq data analyses skills within all Swedish universities. This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data via a series of lectures, group work and computer practicals.

Apply here

Important dates

Application opens:  2018-08-15

Application closes: 2018-09-28

Confirmation to accepted students:  2018-10-06

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 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and snacks.

*Please note that NBIS cannot invoice individuals

Course content

This course will introduce the best practice bioinformatics methods for processing and analyses of ChIP-seq data via a series of lectures, group work and computer practicals.

Topics covered will include:

  • 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 complete the computer exercises

  • Basic knowledge in Linux
  • Ability to bring your own laptop with R installed for the practical exercises
  • Programming/scripting experience, preferably in R

Desirable

  • 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.