title: BM-map: Bayesian mapping of multireads for next-generation sequencing data.
abstract: Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a significant proportion of reads align to multiple genomic locations with equal or similar numbers of mismatches; these are called multireads. The ambiguity in mapping the multireads may lead to bias in downstream analyses. Currently, most practitioners discard the multireads in their analysis, resulting in a loss of valuable information, especially for the genes with similar sequences. To refine the read mapping, we develop a Bayesian model that computes the posterior probability of mapping a multiread to each competing location. The probabilities are used for downstream analyses, such as the quantification of gene expression. We show through simulation studies and RNA-Seq analysis of real life data that the Bayesian method yields better mapping than the current leading methods. We provide a C++ program for downloading that is being packaged into a user-friendly software.
authors.affiliation: Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. yuanj@mdanderson.org
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ji
authors.forename: Yanxun
authors.initials: Y
authors.lastname: Xu
authors.forename: Qiong
authors.initials: Q
authors.lastname: Zhang
authors.forename: Kam-Wah
authors.initials: KW
authors.lastname: Tsui
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yuan
authors.forename: Clift
authors.initials: C
authors.lastname: Norris
authors.forename: Shoudan
authors.initials: S
authors.lastname: Liang
authors.forename: Han
authors.initials: H
authors.lastname: Liang
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001499:Bayes Theorem; D003627:Data Interpretation, Statistical; D008969:Molecular Sequence Data; D012313:RNA / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA