Aim

This workshop aims to provide understanding into ChIP- and ATAC-sequencing. Briefly, the workshop recapitulates the bench workflows, how to prepare your data, call peaks, annotation of peaks in the genome, motif analysis and differential peak analysis. Differences between ChIP-and ATAC-sequencing will be highlighted.

Topics include

• Quick repetition of the workflow/theory of the technique
• Differences between ChIP-seq and ATAC-seq
• Preprocessing (mapping/dealing with genomic repeats etc./removal of low quality alignments)
• Peak calling (Homer/MACS2) – narrow vs. broad peaks. Background in MACS’s peak-building model
• Assessment of peak qualities and reproducibility using IDR method.
• Removal of blacklisted peak regions
• Visualization (Creating bigwigs, heatmaps, histogram plots of peak distributions using DeepTools)
• Motif analysis (Homer/MEME suite, describe the position weight matrix)
• Annotation (Homer and GREAT)
• Differential peak analysis (cover briefly and connect to DESeq2/EdgeR). Usage of BedTools to create count matrix for reads.

The detailed schedule will be distributed to accepted participants prior to the start of the workshop.

Number of participants

5-10

Entry requirements

• Participants are expected to use their own computers.
• Basic knowledge of ChIP-seq and ATAC-seq from wet-lab
• Familiarity with NGS data
• Comfortable in usage of Linux command line (Bash)
• LUNARC account

This workshop is organised by the Research School in Stem Cell Biology in collaboration with the StemTherapy Bioinformatics Core Facility. Please be aware that the number of participants is limited. Participation in the workshop is free of charge for members of the Research School in Stem Cell Biology.