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From FASTQ to Figures — Epigenomics Edition

A self-paced online course built for researchers to learn ChIP-seq, ATAC-seq, CUT&Tag, and DSBCapture data analysis — in short video lessons that fit around a busy research schedule.

Who This Is For

  • You're a researcher generating ChIP-seq, ATAC-seq, CUT&Tag, or DSBCapture data and need to analyze it yourself
  • You've tried following published pipelines but don't fully understand what each tool is doing
  • You want to be able to troubleshoot your own results instead of guessing why peak calling looks wrong
  • You need a course that fits around experiments and deadlines, not a fixed weekly class schedule

How the Course Works

This course runs over several months and is built specifically around the reality of a doctoral candidate's schedule: concise, flexible, and self-paced.

  • Each module is broken into several short videos, typically 10–15 minutes each — watch whenever you have time, not when a schedule dictates
  • Most videos end with questions and exercises to deepen understanding before moving on
  • Regular live Q&A sessions via Zoom — ask questions, discuss exercises, and work through your own data with guidance
  • Rolling enrollment — join at any time, no need to wait for a fixed start date
  • Once enrolled, you keep access with an ongoing monthly live Q&A session — so support doesn't stop once you've finished the videos

What You'll Learn

Introductory Session

Introduction to the platform and the course concept — what to know before getting started.

Module 1 — Introduction to Unix

Useful commands, installing programs, and how to work with high-performance clusters.

Module 2 — From FASTQ Files to Count Matrix

Quality control, adapter trimming, alignment, peak calling, and count matrix generation.

Module 3 — From Count Matrix to Differentially Enriched Regions

Introduction to R, and differential analysis across two or more conditions.

Module 4 — Further Analysis Options

Bigwig files and the IGV browser, profiles and heatmaps, gene annotation, transcription factor binding sites, copy number aberrations, and pairwise interval comparisons (Intervene).

 

Equally suitable for ChIP-seq, CUT&Tag, DSBCapture, and ATAC-seq data — the workflow covers what's shared across all four, with method-specific notes where they differ.

Format

  • Short video lessons (10–15 min each) — rewatch anytime, work through at your own pace
  • Questions and exercises after most videos to reinforce what you've learned
  • Live Zoom Q&A sessions — regular during the course, then monthly on an ongoing basis
  • Rolling enrollment — start whenever you're ready, no fixed cohort start date
  • Mode of instruction: English
Contact us

Your Trainer

Dr. Michaela Höhne-Wiechmann

Biologist by training, she moved into bioinformatics toward the end of her PhD and throughout her postdoc — teaching herself along the way, detours and frustration included. Today, she works as a Scientist in Bioinformatics at TRON gGmbH in Mainz, where she's the go-to expert for RNA-seq analysis and training. She has also built and maintains an internal R package for differential expression analysis.

It's exactly that self-taught experience that shaped this course: built by a biologist, for biologists, so you can finally analyze — and truly understand — your own data.

Get in touch

“Simply awesome! I learned a lot about ChIP-Seq, HPC, and plotting beautiful plots in R... highly recommended” 

Bachuki Shashikadze - PhD Candidate QBM LMU Munich

I liked the short intro at the beginning of every video and wrapping up what we did at the end. I liked how the teacher was explaining the process, her pace, and vocabulary used (if there was a strange term, it was explained) but also the voice and intonation made the videos pleasant to listen to (this really shouldn't be underestimated). I liked that the training was divided into smaller pieces, the videos were of perfect length. I liked that there was always a script attached, which I can use, modify, adjust to my needs and I can train with it. I liked that we could always ask a question and we received a fast answer. The Q&A sessions were a very good idea so we could hear somebody else's questions as well.

PhD Candidate - CECAD University of Cologne

I participated in the course ChIP-Seq analysis. Very well prepared, informative videos, covering many tools, well explained. Highly recommended!

 Samantha F - University of Cologne