title: NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets.
abstract: The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France. marco@igbmc.fr.
authors.forename: Marco Antonio
authors.initials: MA
authors.lastname: Mendoza-Parra
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France.
authors.forename: Mohamed-Ashick M
authors.initials: MA
authors.lastname: Saleem
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Blum
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France.
authors.forename: Pierre-Etienne
authors.initials: PE
authors.lastname: Cholley
authors.affiliation: Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France.
authors.forename: Hinrich
authors.initials: H
authors.lastname: Gronemeyer
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods; D019295:Computational Biology / Q000379:methods* / Q000592:standards; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods* / Q000592:standards; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D064878:Web Browser
keywords: ChIP-sequencing; Database; Galaxy; Massive parallel sequencing; Next-generation sequencing; Quality control