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

Lausanne, 27 April - 1 May 2015

Data reproduction exercise: nucleosome signal in promoters.

Author: Rene Dreos

Introduction

This exercise is based on the following paper: The autors analysed transcription initiation events using CAGE technology in many human and mouse primary tissues and cell lines.

Exercise

We wil try to reprocude results shown in Figure S2d as in (FANTOM Consortium 2014).

Figure S2d:

The autors classified promoters based on their initiation pattern into two classes: broad and sharp. They then studied the base composition around them. They found a characteristic signal in the region +50 to +200 bp from the TSS that show a strong periodic signal. This signal is similar to the one from MNase-seq experiments of region with high nucleosome affinity.

Hints and recipes

Note that the data used in this paper is present on the ChIP-Seq server, aligned on hg19 genome assembly.
To reproduce the figures you should: