This tutorial assumes that you are familiar with the concepts developed in the following parts of the theoretical course.
It is better to follow the corresponding tutorials before this one.
A companion tutorial explains how to retrieve peak sequences from Galaxy.
The RSAT software suite includes a set of powerful tools allowing to analyse motifs in peak sets obtained from ChIP-seq and related methods. The goal of this tutorial is to provide a short introduction of these tools, and show how they can be combine to extract the best of your chip-seq peaks.
peak-motifs | A workflow integrating a series of pre-existing tools for motif discovery (oligo-analysis, dyad-analysis, position-analysis, local-word-analysis), which enables to discover motifs in ChIP-seq peak sequences, compare the motifs scan the peaks to detect putative binding sites. The accuracy and time-efficiency of the workflow have been described in detail (Thomas-Chollier et al., 2012a. Nucleic Acids Res 40: e31), and a detailed protocol has been published (Thomas-Chollier et al., 2012, Nat Protoc 7(8): 1551-1568). |