Systematic Regional Bias is Widespread in ChIP-seq (opens in new tab)

Robust and reproducible results are essential for confident scientific analysis. We demonstrate that transcription factor (TF) Chromatin Immunoprecipitation coupled with sequencing (ChIP-seq) suffers from systematic bias that may threaten its reproducibility: 80% of 200+ condition-matched, dual-replicate experiments in ENCODE contain genomic regions of systematic bias. We observe this regional bias even between replicates produced within the same experiment, resulting in thousands of unreplic...