Regions that contain a binding site for the DNA-binding protein of interest will be indicated by higher sequencing read density. Because single-end reads each only cover one end of a larger sequence fragment, enriched regions will generally show two adjacent peaks. Using the effective fragment length calculated using Cross Strand-Correlation, Partek Genomics Suite will extend each read in the 3' direction by the effective fragment length and merge overlapping extended reads into a single peak. For paired-end reads, the distance between paired reads is used as the fragment length and overlapping fragments are merged into peaks. For peak detection, Partek Genomics Suite divides the genome into windows (bins) of a user-defined size and counts the number of fragments that fall within each bin. Partek Genomics Suite fits a zero-truncated negative binomial to the bin counts and finds all regions that are above a user-defined false discovery rate (FDR). See the ChIP-Seq white paper for more information on the peak-finding algorithm and tips for setting the Fragment extension and window sizes. 

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