Welcome to the Epigenomics tutorial documentation!

If you are taking part in our tutorial, then you find the information here that you need. The documentation is split up into 4 parts. Make sure to read and follow the **What you need part** with all necessary Installations before you join us virtually. Below you can see an illustration of the workflow we planned for you.

PDF of the flowchart

Contents:

• What you need
  • Download docker image
  • How to access data inside the docker container
  • How to remove all the containers and images after the tutorial
• Practical I - Detection of Open Chromatin regions & Footprint calling & Transcription factor prediction
  • Example data
  • Step 1: Quality check, aligment and peak calling of ATAC-seq data
  • Step 2: Footprint calling
  • Step 3: TF binding site prediction
  • Step 4: Average footprint profiles and differential activity analysis
• Practical II - Linking regions to genes and integration with gene expression data
  • Step 1: Extracting TF motifs of TFs expressed in the cell types of interest
  • Step 2: Intersect the footprint from HINT with differentially ATAC-peaks
  • Step 3: Deriving candidate transcriptional regulators using DYNAMITE
• Practical III - Target gene identification of candidate regions
  • Step 1: Fetching candidate regions
  • Step 2.1: Target genes - Nearest gene
  • Step 2.2: Target genes - Window-based approach
  • Step 2.3: Target genes - Association-based approach
  • Step 3: Intersecting the identified target genes
  • Step 4: All steps in one