ChIP-Center Analysis Module

ChIP-Center shifts mapped positions of selected ChIP-tag reads to estimated center-positions of DNA fragments.
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.
In order to avoid repeated transfer of large files, the ChIP-centering function is also provided as 'Additional Input Data Option' in the input form of all ChIP-Seq web tools.
The output is a SGA-formatted file representing the positions of the centered tags. Optionally, a wiggle (WIG) track file, in compressed format, can be generated for uploading results to the UCSC genome browser. For supported genome assemblies, direct links to the UCSC genome browser are also provided for rapid comparison with genome annotations.

 Zebrafish sample profile of nucleosome organization around the promoter of supt6h at the 256-cell stage (as displayed in Fig. 1.A, in Zhang et al., Genome Research 2014).

 Zebrafish sample profile of nucleosome organization around the promoter of supt6h at the dome stage (as displayed in Fig. 1.A, in Zhang et al., Genome Research 2014).