Epigenomics Data Analysis: from Bulk to Single Cell – ONLINE
September 16, 2024 @ 08:00 – September 20, 2024 @ 17:00 CEST
National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of Epigenomics data analysis skills. We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!
Important dates and information
Application opens: 2024-04-26
Application closes: 2024-08-28
Confirmation to accepted students: 2024-08-30
Course Leaders : Agata Smialowska and Louella Vasquez
Contact information: edu.epigenomics@nbis.se
Course fee
This online training event has no fee for academic participants. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 2 000 SEK. For non-academic participants a course fee* of 12 000 SEK will be invoiced.
*Please note that NBIS cannot invoice individuals
Course content
This workshop aims to introduce the best practice bioinformatics methods for processing, analyses, visualisation and integration of epigenomics and functional genomics data.
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.
Entry requirements
Required for being able to follow the workshop 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.
Desirable:
- Experience working on the SNIC center Uppmax or another HPC. We encourage participants to run the linked Uppmax tutorial before the workshop;
- Previous experience with NGS data analyses;
- Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Foundations for Life Scientists” or equivalent.
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.
Link to application
https://forms.gle/BbmWmLwZFS1ed8EeA
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