Nanocourse: Data Analysis for ChIP-Seq and similar techniques

In this nanocourse, you will learn theoretical and practical aspects of ChIP-Seq and similar techniques and how to apply them for your research.

Please register for this course by emailing gindrat@molgen.mpg.de.

The nanocourse is open to all interested people.

Program

Thursday, 25.01.2024 (SR1 MPIMG)

09.00 – 10.00: ChIP-seq peak calling and MACS (Martin Vingron) → differences between HM ChIP and TF ChIP profiles, normalization methods, peak calling with and w/o control

10.00 – 11.00: ATAC peak calling (and footprinting) (Yufei Zhang)

Negative Binomial distribution, alternative peak caller for ChIP-seq, ATAC-seq & TF footprinting

11.00 – 12.00: CUT&TAG (+ Spike-In) + Cut and run? (Persia Akbari-Omgba)

12.00 – 14.00: Lunch break

14.00 – 15.30: Nascent RNA sequencing: protocols and peak calling (Andreas Mayer, Mario Rubio)

15:30 – 16:00: Questions and instruction for the second day, pair up for the second day

Friday, 26.01.2024, Practical work (PR room MPIMG)

Instructors: Yufei, Mario, Helene, Persia

1) Processing and analysing

09.00 – 10.00: Introductions :

Working with ChIP data on our cluster (codes for preprocessing: Yufei)

QC with IGV (Helene)

Deeptools (Mario)

Differential peak detection (Mario)

10.00 – 12.00: Processing of H3K4me3 ChIP with and without input for two biological conditions

Data Visualization

12.00 – 13.00: Discussion of the morning results

13.00 – 14.00: Lunch break

2) Blinded ChIP game

14.00 – 15.30: Use tools from before to determine which unlabelled Peak and Signal files are what

Before signing up for this nanocourse, please make sure that you can attend all the dates and write them in your calendar. If you do not show up or cancel at very short notice, other interested students will not be able to participate.