RT Journal Article
SR Electronic
T1 Ritornello: High fidelity control-free chip-seq peak calling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 034090
DO 10.1101/034090
A1 Kelly Patrick Stanton
A1 Jiaqi Jin
A1 Sherman Weissman
A1 Yuval Kluger
YR 2015
UL http://biorxiv.org/content/early/2015/12/10/034090.abstract
AB With the advent of next generation high-throughput DNA sequencing technologies, omics experiments have become the mainstay for studying diverse biological effects on a genome wide scale. ChIP-seq is the omics technique that enables genome wide localization of transcription factor binding or epigenetic modification events. Since the inception of ChIP-seq in 2007, many methods have been developed to infer ChIP target binding loci from the resultant reads after mapping them to a reference genome. However, interpreting these data has proven challenging, and as such these algorithms have several shortcomings, including susceptibility to false positives due to artifactual peaks, poor localization of binding sites, and the requirement for a total DNA input control which increases the cost of performing these experiments. We present Ritornello, a new approach with roots in digital signal processing (DSP) that addresses all of these problems. We show that Ritornello generally performs equally or better than the peak callers tested and recommended by the ENCODE consortium, but in contrast, Ritornello does not require a matched total DNA input control to avoid false positives, effectively decreasing the sequencing cost to perform ChIP-seq.