Chip-seq data analysis: from quality check to motif discovery and more

Lausanne, 27 April - 1 May 2015

Data reproduction exercise: Nucleosome distribution around promoters.

Author: Rene Dreos


This exercise is based on the following paper: The autors analysed varous histone modification and variants distributions around promoters stratified by their initiation pattern.
The metilated histones and the variant H2A.Z were initially published in: Histone H3 was from: and acetylated histones from:


We wil try to reprocude results shown in Figure 1a,b; Figure 2 and FIgure 3 in (Nozaki et al. 2011).

Figure 1:
Figure 2:
Figure 3:

Have a look at the Figure legends and the Methods section of the corresponding paper. The autors classified promoters based on their initiation pattern into two classes: broad and peak. They then studied the chromatin organisation around the two promoter classes. Figure 1A,B and Figure 2 show similar things: the distribution around the two promoter classes of several histone marks. Figure 3 instead shows the ratio (look in the paper for the exact definition) of the distribution of the two classes for each histone mark.
Once you have found the results you can check if the conclusion reported in the paper holds:

Hints and recipes

Note that the data used in this paper is present on the ChIP-Seq server, aligned on hg18 genome assembly.
To reproduce the figures you should: