Section outline

  • 9:15 Theoretical part (60-90 min)

    Principles of ChIP-Seq data analysis: a practical approach. Focus will be given to bioinformatics pipeline for quality controls, peak detection, annotation and functional analysis.

    10:30 Coffee break

    11:00 Practical (RStudio and terminal, in Linux Virtual Machine)

    Run QC tools (deepTools, ChIPQC), apply peak calling (MACS2), annotate the peaks (ChIPseeker), plot peak profiles and TSS heatmaps (ChIPseeker), differential binding analysis with DiffBind. Finally add the RNA-seq analysis information.

    12:30 Lunch break

    13:30 practical session 2 

    15:00 Coffee break

    15:30 practical session 2