ActionsCite Favorites Display options Display options Format Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization 1 Department of Molecular Virology, Immunology Medical Genetics, The Ohio State University, Columbus, OH, USA. Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization 1 Department of Molecular Virology, Immunology Medical Genetics, The Ohio State University, Columbus, OH, USA. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a high-throughput antibody-based method to study genome-wide protein-DNA binding interactions. ChIP-seq technology allows scientist to obtain more accurate data providing genome-wide coverage with less starting material and in shorter time compared to older ChIP-chip experiments. Herein we describe a step-by-step guideline in analyzing ChIP-seq data including data preprocessing, nonlinear normalization to enable comparison between different samples and experiments, statistical-based method to identify differential binding sites using mixture modeling and local false discovery rates (fdrs), and binding pattern characterization. In addition, we provide a sample analysis of ChIP-seq data using the steps provided in the guideline. Ma W, et al. Methods Enzymol. 2011;497:51-73. doi: 10.1016/B978-0-12-385075-1.00003-2. Methods Enzymol. 2011. PMID: 21601082 Methods Mol Biol. 2010;674:143-59. doi: 10.1007/978-1-60761-854-6_9. Methods Mol Biol. 2010. PMID: 20827590 Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL. Laajala TD, et al. BMC Genomics. 2009 Dec 18;10:618. doi: 10.1186/1471-2164-10-618. BMC Genomics. 2009. PMID: 20017957 Free PMC article. Hoffman BG, et al. J Endocrinol. 2009 Apr;201(1):1-13. doi: 10.1677/JOE-08-0526. Epub 2009 Jan 9. J Endocrinol. 2009. PMID: 19136617 Park PJ. Nat Rev Genet. 2009 Oct;10(10):669-80. doi: 10.1038/nrg2641. Epub 2009 Sep 8. Nat Rev Genet. 2009. PMID: 19736561 Free PMC article. Review. Park J, et al. Comput Struct Biotechnol J. 2015 May 21;13:366-9. doi: 10.1016/j.csbj.2015.05.002. eCollection 2015. Comput Struct Biotechnol J. 2015. PMID: 26106460 Free PMC article. Angelini C, et al. BMC Bioinformatics. 2015 May 9;16:150. doi: 10.1186/s12859-015-0579-z. BMC Bioinformatics. 2015. PMID: 25957089 Free PMC article. Kennedy PG, et al. J Gen Virol. 2015 Jul;96(Pt 7):1581-602. doi: 10.1099/vir.0.000128. Epub 2015 Mar 20. J Gen Virol. 2015. PMID: 25794504 Free PMC article. Review. Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J. Bailey T, et al. PLoS Comput Biol. 2013;9(11):e1003326. doi: 10.1371/journal.pcbi.1003326. Epub 2013 Nov 14. PLoS Comput Biol. 2013. PMID: 24244136 Free PMC article. BMC Bioinformatics. 2013 May 30;14:169. doi: 10.1186/1471-2105-14-169. BMC Bioinformatics. 2013. PMID: 23721376 Free PMC article.