statistical issues in the analysis of chip-seq and rna-seq data统计问题分析chip-seq和rna-seq数据.pdf

Genes 2010, 1, 317-334; doi:10.3390/genes1020317 OPEN ACCESS genes ISSN 2073-4425 /journal/genes Review Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data Debashis Ghosh 1,* and Zhaohui S. Qin 2 1 Department of Statistics and Public Health Sciences, Penn State University, 514A Wartik Building, University Park, PA 16802, USA 2 Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Center for Comprehensive Informatics, Emory University, 1518 Clifton Rd., N.E., Atlanta, GA 30322, USA; E-Mail: zhaohui.qin@ * Author to whom correspondence should be addressed; E-Mail: ghoshd@; Tel.: +1-814-933-9601; Fax: +1-814-863-6699. Received: 17 August 2010 / Accepted: 20 September 2010 / Published: 27 September 2010 Abstract: The recent arrival of ultra-high throughput, next generation sequencing (NGS) technologies has revolutionized the genetics and genomics fields by allowing rapid and inexpensive sequencing of billions of bases. The rapid deployment of NGS in a variety of sequencing-based experiments has resulted in fast accumulation of massive amounts of sequencing data. To process this new type of data, a torrent of increasingly sophisticated algorithms and software tools are emerging to help the analysis stage of the NGS applications. In this article, we strive to comprehensively identify the critical challenges that arise from all stages of NGS data analysis and