Brief. Bioinformatics - Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts.

Tópicos

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Resumo

The current understanding of the regulation of transcription does not keep the pace with the spectacular advances in the determination of genomic sequences. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) promises to give better insight into transcription regulation by locating sites of protein-DNA interactions. Such loci of putative interactions can be inferred from the genome-wide distributions of ChIP-seq data by peak-calling software. The analysis of ChIP-seq data critically depends on this step and a multitude of these peak-callers have been deployed in the recent years. A recent study reported severe variation among peak-calling results. Yet, peak-calling still lacks systematic quantitative benchmarking. Here, we summarize benchmarking efforts and explain potential drawbacks of each benchmarking method.

Resumo Limpo

current understand regul transcript keep pace spectacular advanc determin genom sequenc chromatin immunoprecipit follow massiv parallel sequenc chipseq promis give better insight transcript regul locat site proteindna interact loci putat interact can infer genomewid distribut chipseq data peakcal softwar analysi chipseq data critic depend step multitud peakcal deploy recent year recent studi report sever variat among peakcal result yet peakcal still lack systemat quantit benchmark summar benchmark effort explain potenti drawback benchmark method

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