Wiki

Welcome to the Helmholtz Summer School on Chromatin Biology: A hands-on expedition

Resources

9.00 Welcome (Tamas)
9.10 Reproducible Research (lecture, Tamas ~1hr)
10.30 Setup VS Code (workshop, Elizabeth ~30 min)
11.00 Introduction
- Beginner (workshop, Elizabeth and Marlies ~1.5hr):
  - Introduction to the Command Line (Elizabeth)
  - HPC/slurm (Marlies), Conda (Marlies)
  - Snakemake short introduction (Elizabeth)
- Experienced (Gabriela and Tamas ~1.5hr)
  - Workflow management (lecture, Gabriela ~25min)
  - Snakemake Tutorial (workshop, Gabriela and Tamas ~1hr)
12.30 Lunch
13.30 Seminar
14.30 Workflow Steps (lecture, Tamas ~1hr)
15.30 Data Processing (workshop, Tamas ~1.5hr)
- Quality Control
- Alignment
- File formats

9.00 Snakemake Pipeline (~30 min)
9:45 Chromatin Profiling Methods (lecture, Marlies ~15 min)
10.00 Deeptools (workshop, Marlies ~2hr)
- Genome Coverage
- Profile Plots
- Heatmaps
- Correlation analysis
12.30 Lunch
13.30 Seminar
14.30 Peak Finding (workshop, Tamas ~1.5hr)
- MACS2
- Optional: Homer
16.00 Motif Analysis (workshop, Franziska ~1.5hr)
- Homer
- MEME

9.00 R part I (workshop, Franziska and Marika)
- Introduction to R, Rmarkdown and R projects
- Introduction to functions in R
- Working with Peaks in R
  - Introduction to GenomicRanges
  - Peak Overlaps
13.00 Lunch
14.00 Seminar
15.00 R part II (workshop, Franziska and Marika)
- Peak Annotation
- Over-representation analysis (Get meaning out of your peaks)
- Motif Analysis with R
18.00 Seminar

9.00 Differential Analysis (workshop, Tamas ~1.5hr)
- Case study introduction (Marlies ~15 min)
- Normalisation Methods
- DESeq2 analysis
10:30 Advanced Design for differential analysis (discussion, Franziska)
11.00 Pipeline Results (discussion, Tamas ~1.5 hr)
12.30 Lunch
13.30 Seminar
14.30 Final Project (discussion, Gabriela ~3 hr)
- Talk Preparation