This workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.

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Topics covered include:

• Data processing and analyses for differential DNA methylation with Illumina EPIC arrays and Bisulfite-seq;
• ChIP-seq: peak calling, peak independent / dependent quality metrics, differential binding analysis; DNA motif enrichment;
• ATAC-seq: peak calling, peak independent / dependent quality metrics, differential accessibility analysis;
• Quantitative ChIP-seq using spike-ins;
• CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;
• Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;
• Basic multi-omics exploration and integration;
• Visualisations of epigenomics datasets;
• Introduction to analysis of single cell functional genomics data (scATAC-seq);
• Introduction to nf-core pipelines for processing and analysis of epi- and functional genomics data : Methylseq, ChIP-seq, ATAC-seq.

Important dates and information

Application opens: 2025-04-28
Application closes: 2025-08-25
Confirmation to accepted students: 2025-08-29

Course fee

This online training event is subsidized by academic grants and thereby free of charge for academic participants. The fee for non-academic participants is 12 000 SEK.

No-show fee: If you accept a position at the workshop but fail to attend without a valid reason (sickness or urgent family matter), you will be liable for a now-show fee of 2 000 SEK (for academic participants) or the full fee (for non-academic participants).

*Please note that NBIS cannot invoice individuals

Due to limited space the course can accommodate a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.