Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
Brief Bioinform. 2022 Jan 17;23(1). doi: 10.1093/bib/bbab537.
Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a technique used to identify protein-DNA interaction sites through antibody pull-down, sequencing and analysis; with enrichment 'peak' calling being the most critical analytical step. Benchmarking studies have consistently shown that peak callers have distinct selectivity and specificity characteristics that are not additive and seldom completely overlap in many scenarios, even after parameter optimization. We therefore developed ChIP-AP, an integrated ChIP-seq analysis pipeline utilizing four independent peak callers, which seamlessly processes raw sequencing files to final result. This approach enables (1) better gauging of peak confidence through detection by multiple algorithms, and (2) more thoroughly surveys the binding landscape by capturing peaks not detected by individual callers. Final analysis results are then integrated into a single output table, enabling users to explore their data by applying selectivity and sensitivity thresholds that best address their biological questions, without needing any additional reprocessing. ChIP-AP therefore presents investigators with a more comprehensive coverage of the binding landscape without requiring additional wet-lab observations.
染色质免疫沉淀结合测序（ChIP-seq）是一种通过抗体下拉、测序和分析来识别蛋白-DNA 相互作用位点的技术；富集“峰”调用是最关键的分析步骤。基准测试研究一致表明，峰调用器具有不同的选择性和特异性特征，在许多情况下，即使在参数优化后，它们也不是可加的，很少完全重叠。因此，我们开发了 ChIP-AP，这是一个利用四个独立的峰调用器的集成 ChIP-seq 分析管道，它可以无缝地处理原始测序文件以获得最终结果。这种方法可以通过多种算法检测来（1）更好地衡量峰的可信度，并且（2）通过捕获单个调用器未检测到的峰来更全面地调查结合景观。最终的分析结果将整合到一个单一的输出表中，使用户能够通过应用最能解决其生物学问题的选择性和敏感性阈值来探索他们的数据，而无需进行任何额外的重新处理。因此，ChIP-AP 为研究人员提供了更全面的结合景观覆盖范围，而无需进行额外的湿实验室观察。
