Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

摘要: Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA interactions. Identification of protein binding sites from ChIP-seq data has required novel computational tools, distinct those used for the analysis ChIP-Chip experiments. The growing popularity spurred development many different analytical programs (at last count, we noted 31 open source methods), each some purported advantage. Given that literature dense and empirical benchmarking challenging, selecting an appropriate method become a daunting task. Herein compare performance eleven peak calling on common empirical, transcription factor datasets measure their sensitivity, accuracy usability. Our provides unbiased critical assessment available technologies, should assist researchers in choosing suitable tool handling data.