Epigenomics Data Analysis: from Bulk to Single Cell

Description

The aim of this workshop is to introduce best practice bioinformatics methods for processing, analyses and integration of epigenomics data. The online teaching includes lectures, programming tutorials and interactive group sessions. This workshop is run by the National Bioinformatics Infrastructure Sweden (NBIS).

Topics covered

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

Topis 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;
• Functional analysis, including finding nearest genes and custom features, GO terms and Reactome pathways enrichment;
• Quantitative ChIP-seq;
• CUT&Tag / CUT&RUN: Novel methods to investigate protein-chromatin interactions;
• Integrative visualisations of epigenomics datasets;
• Basic multi-omics exploration and integration;
• Introduction to analysis of single cell functional genomics data (scATAC-seq);
• Nf-cores pipelines: Methylseq, ChIP-seq, ATAC-seq

Pre-requisites

Minimal requirements to be able to follow the tutorials:

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

Desired, to make learning experience easier:

• Experience working on the SNIC center Uppmax or another HPC
• Previous experience with NGS data analyses
• Completing NBIS workshops “Introduction to Bioinformatics using NGS data” and “R Foundations for Life Scientists” or equivalent

Level

intermediate