A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs - Archive ouverte HAL Access content directly
Journal Articles Nature Protocols Year : 2012

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs

Morgane Thomas-Chollier
Elodie Darbo
  • Function : Author
Carl Herrmann
  • Function : Author
Matthieu Defrance
  • Function : Author
Denis Thieffry

Abstract

This protocol explains how to use the online integrated pipeline 'peak-motifs' (http://rsat.ulb.ac.be/rsat/) to predict motifs and binding sites in full-size peak sets obtained by chromatin immunoprecipitation-sequencing (ChIP-seq) or related technologies. The workflow combines four time-and memory-efficient motif discovery algorithms to extract significant motifs from the sequences. Discovered motifs are compared with databases of known motifs to identify potentially bound transcription factors. Sequences are scanned to predict transcription factor binding sites and analyze their enrichment and positional distribution relative to peak centers. Peaks and binding sites are exported as BED tracks that can be uploaded into the University of California Santa Cruz (UCSC) genome browser for visualization in the genomic context. This protocol is illustrated with the analysis of a set of 6,000 peaks (8 Mb in total) bound by the Drosophila transcription factor Kruppel. The complete workflow is achieved in about 25 min of computational time on the Regulatory Sequence Analysis Tools (RSAT) Web server. This protocol can be followed in about 1 h.

Dates and versions

hal-01624286 , version 1 (26-10-2017)

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Cite

Morgane Thomas-Chollier, Elodie Darbo, Carl Herrmann, Matthieu Defrance, Denis Thieffry, et al.. A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nature Protocols, 2012, 7 (8), pp.1551-1568. ⟨10.1038/nprot.2012.088⟩. ⟨hal-01624286⟩

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