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chippeak description

Chippeak locates signal peaks in ChIP-Seq data targeted at transcription factors. The input is a set of tag read positions produced by a ChIP-Seq experiment mapped to a reference genome. A working format is a simplified GFF format, called SGA, which is sorted by sequence name and position. In addition to SGA, ChIP-Peak supports other input data formats such as BED, GFF, BAM, and FPS. Compressed input data in gzip or zip format is also accepted. ChIP-peak returns peak center positions and is typically used for detecting transcription factor binding sites. If *peak refinement* is selected, a post-processing method will recompute the peak position with higher precision within all detected peak windows. ChIP-Peak returns results in various formats: SGA-formatted file, which is the default output of the program, and, provided the species is supported, FPS-formatted file. The output is further provided as a wiggle (WIG) track file, in compressed format, which can be uploaded to the UCSC geneome browser via direct link from the ChIP-Peak result page. As a further option, sequences around peak locations can be extracted to a file in FASTA format. Sequence extraction is carried out using the FPS-formatted output.

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.