下一代测序中ChIP-seq数据的处理与分析

doi:10.3724/SP.J.1005.2012.00773

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HEREDITAS ›› 2012, Vol. 34 ›› Issue (6): 773-783.doi: 10.3724/SP.J.1005.2012.00773

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Processing and analysis of ChIP-seq data

GAO Shan¹, ZHANG Ning¹, LI Bo², XU Shuo³, YE Yan-Bo⁴, RUAN Ji-Shou¹

1. College of Mathematics, Nankai University, Tianjin 300071, China 2. College of Bioengineering, Chongqing University, Chongqing 400044, China 3. Institute of Scientific and Technical Information of China, Beijing 100038, China 4. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

Received:2011-10-10 Revised:2011-12-04 Online:2012-06-20 Published:2012-06-25

Abstract

Abstract: The next-generation sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is becoming a key technology for the study of transcriptional regulation in the context of functional genomics. Due to the overwhelming amount of data generated from ChIP-seq experiments, the ChIP-seq data processing brings many new challenges in the field of bioinformatics. Considering the development of data processing skills largely behind that of the ChIP-seq experiment techniques, it is urgent to give a review on the ChIP-seq data processing for more and more oncoming researchers to build or improve algorithms. This paper provides a brief overview of the ChIP-seq data processing, highlighting the main prob-lems and methods in detail, to allow scientists to understand rapidly and deeply.

Key words: next generation sequencing, ChIP-seq, data process, transcription regulation, epigenetics

GAO Shan, ZHANG Ning, LI Bo, XU Shuo, YE Yan-Bo, RUAN Ji-Shou. Processing and analysis of ChIP-seq data[J]. HEREDITAS, 2012, 34(6): 773-783.

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