RSA-tools - Tutorials - peak-motifs

Contents

  1. Prerequisite
  2. Introduction
  3. References


Prerequisite

This tutorial assumes that you are familiar with the concepts developed in the following parts of the theoretical course.

  1. PSSM theory
  2. String-based motif discovery

It is better to follow the corresponding tutorials before this one.

  1. Position-specific scoring matrices.
  2. oligo-analysis: detection of over-represented words.
  3. position-analysis: detection of words having a positional bias in sequences aligned on some reference position.

A companion tutorial explains how to retrieve peak sequences from Galaxy.


Introduction

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).


References

  1. Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568. [PMID 22836136]
  2. Thomas-Chollier, M., Herrmann, C., Defrance, M., Sand, O., Thieffry, D. and van Helden, J. (2011). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets Nucleic Acids Research doi:10.1093/nar/gkr1104, 9. [Open access]

For suggestions or information request, please contact Morgane Thomas-Chollier or Jacques van Helden