PeakSeq

Chromatin immunoprecipitation (ChIP) followed by tag sequencing (ChIP-seq) is a fast and preferred approach for mapping sites of transcription-factor binding and chromatin modification. However, it presents unique challenges in data analysis, such as signals caused by open chromatin.

PeakSeq utilizes a general scoring approach that is based on the observation that sites of potential binding are strongly correlated with signal peaks in the control, which likely reveals features of open chromatin. To address this, the tool employs a two-pass strategy that compensates for the signal caused by open chromatin, as revealed by the inclusion of controls.

In the first pass, PeakSeq identifies putative binding sites and compensates for genomic variation in the 'mappability' of sequences. Meanwhile, the second pass filters out sites not significantly enriched compared to the normalized control, computing precise enrichments and significances. This scoring procedure enables researchers to optimize the experimental design by estimating the depth of sequencing required for a desired level of coverage. Moreover, it shows that more than two replicates provide only a marginal gain in information.

With its unique approach and strategy, PeakSeq helps researchers to overcome the challenges of analyzing ChIP-seq data.