Chipscore is a feature extraction tool for ChIP-seq data analysis. It reads a ChIP-seq data file in SGA format, and compares two features, a reference feature (feature A) and a target feature (feature B), with respect to their relative position. By default, the program extracts feature A tags that are enriched in feature B tags according to a given count output threshold or score that is 0 by default. If option -r is specified, the program extracts sites that are depleted in feature B. The feature specification must have the following format:
Parent program: chip-seq
ChIP-Seq combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify the set of cis-acting targets of DNA-associated proteins or factors on a genome scale. It can be used to precisely map global binding sites for any protein of interest. Previously, ChIP-on-Chip was the most common technique used to identify trascription factor DNA interactions. Chip-Seq is also used to study epigenetic events such as histone modifications and DNA methylation.