Chipcor reads ChIP-Seq tag positions and generates a positional correlation histogram for two genomic features. Input features maybe ChIP-Seq tag positions, peaks found by Chip_Peak, or any type of genome annotation data that can be mapped to a single base on the genome. The input of ChIP-Cor is a set of tag positions mapped to a reference genome produced by a ChIP-Seq experiment.A simplified GFF format, called SGA (Simplified Genome Annotation), which is sorted by sequence name and position is used in Chipcor. In addition to SGA, ChIP-Cor supports other input data formats such as BED, GFF, BAM, and FPS. Compressed input data in gzip or zip format is also accepted. The output is a tag correlation histogram showing the abundance of the *target* feature as a function of the distance from the *reference* feature. At output, we also provide a *feature extraction* option that includes DNA sequence extraction for selecting ChIP-enriched regions of interest.
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.