Chipcenter shifts tags mapping to the *+* or *-* strand towards the expected center of tha DNA fragment. The input is a set of tags positions produced by a ChIP-Seq experiment mapped to a reference genome. The default working format is a simplified GFF format, called SGA, which is sorted by sequence name and position. In addition to SGA, ChIP-Center supports other input data formats such as BED, GFF, BAM, and FPS. Compressed input data in gzip or zip format is also accepted. The optimal tag shift distance can be inferred as half of the predominant fragment length, as obtained from the correlation analysis (by ChIP-Cor) of tags mapping to the positive strand against tags mapping to the negative strand.
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.