TY - JOUR T1 - A comparison of peak callers used for DNase-seq data JF - bioRxiv DO - 10.1101/003608 SP - 003608 AU - Hashem Koohy AU - Thomas A. Down AU - Mikhail Splivakov AU - Tim Hubbard Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/03/27/003608.abstract N2 - Genome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements. A variety of algorithms have been developed to identify regions of open chromatin from raw sequence-tag data so it is important to assess and compare their performance.In this study, four published publicly available peak calling algorithms for DNase-seq data are assessed at a range of signal thresholds. They are assessed against an independent data set of regulatory regions derived from experimental ENCODE transcription factor binding data for each particular cell type. The level of overlap between peak regions reported by each algorithm and the ENCODE derived data set are used to assess sensitivity and specificity of the algorithms.Our study suggests that F-seq has a slightly higher sensitivity than the next best algorithms. Hotspot and the ChIP-seq oriented method, MACS, both perform competitively when used with their default parameters. However the generic peak finder ZINBA appears to be less sensitive than the other three.We also show how the accuracy of each algorithm is dependent on the threshold used. In particular, we show that the accuracy of F-Seq can be considerably improved by using different parameters to the default suggested by its developers. ER -