ChIP-Peak Analysis Module

ChIP-Peak locates signal peaks in ChIP-Seq data targeted at transcription factors.
The input is a set of read read positions produced by a ChIP-Seq experiment mapped to a reference genome. We use as a working format a simplified GFF format, called SGA (Simplified Genome Annotation), 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.