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