ChIPulate: A comprehensive ChIP-seq simulation pipeline

Author summary DNA-binding proteins perform many key roles in biology, such as transcriptional regulation of gene expression and chromatin modification. ChIP-seq (Chromatin immunoprecipitation followed by high-throughput sequencing) is a widely used experimental technique to identify DNA-binding sites of specific proteins of interest, within cells, genome-wide. DNA fragments from genomic regions that are bound by a protein of interest, often a transcription factor (TF), are selectively extracted using specific antibodies, amplified using PCR, and sequenced. The sequences are mapped to the reference genome. Regions where many sequences map, called “peaks”, are used to infer the location of TF-bound loci (peaks), in vivo occupancy at those loci, and the sequence pattern (motif) to which the TF shows a binding affinity. But measurements of TF occupancy and motif inference are vulnerable to several biological and experimental sources of variation that are poorly understood and difficult to assess directly. Here, we simulate key steps of the ChIP-seq protocol with the aim of estimating the relative effects of various sources of variations on motif inference and binding affinity estimations. Besides providing specific insights and recommendations, we provide a general framework to simulate sequence reads in a ChIP-seq experiment, which should considerably aid in the development of software aimed at analyzing ChIP-seq data.