title: Interpreting and visualizing ChIP-seq data with the seqMINER software.
abstract: Chromatin immunoprecipitation coupled high-throughput sequencing (ChIP-seq) is a common method to study in vivo protein-DNA interactions at the genome-wide level. The processing, analysis, and biological interpretation of gigabyte datasets, generated by several ChIP-seq runs, is a challenging task for biologists. The seqMINER platform has been designed to handle, compare, and visualize different sequencing datasets in a user-friendly way. Different analysis methods are applied to understand common and specific binding patterns of single or multiple datasets to answer complex biological questions. Here, we give a detailed protocol about the different analysis modules implemented in the recent version of seqMINER.
authors.affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104 CNRS, UdS, INSERM U964, BP 10142, F-67404 ILLKIRCH Cedex, CU de Strasbourg, France.
authors.forename: Tao
authors.initials: T
authors.lastname: Ye
authors.forename: Sarina
authors.initials: S
authors.lastname: Ravens
authors.forename: Arnaud R
authors.initials: AR
authors.lastname: Krebs
authors.forename: Làszlò
authors.initials: L
authors.lastname: Tora
mesh_terms: D056808:Biostatistics / Q000379:methods*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016000:Cluster Analysis; D003196:Computer Graphics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012984:Software