title: A new approach to bias correction in RNA-Seq.
abstract: BACKGROUND
  Quantification of sequence abundance in RNA-Seq experiments is often conflated by protocol-specific sequence bias. The exact sources of the bias are unknown, but may be influenced by polymerase chain reaction amplification, or differing primer affinities and mixtures, for example. The result is decreased accuracy in many applications, such as de novo gene annotation and transcript quantification.
  
  
  RESULTS
  We present a new method to measure and correct for these influences using a simple graphical model. Our model does not rely on existing gene annotations, and model selection is performed automatically making it applicable with few assumptions. We evaluate our method on several datasets, and by multiple criteria, demonstrating that it effectively decreases bias and increases uniformity. Additionally, we provide theoretical and empirical results showing that the method is unlikely to have any effect on unbiased data, suggesting it can be applied with little risk of spurious adjustment.
  
  
  BACKGROUND
  The method is implemented in the seqbias R/Bioconductor package, available freely under the LGPL license from http://bioconductor.org
  
  
  BACKGROUND
  dcjones@cs.washington.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. dcjones@cs.washington.edu
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Jones
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
authors.forename: Xinxia
authors.initials: X
authors.lastname: Peng
authors.forename: Michael G
authors.initials: MG
authors.lastname: Katze
mesh_terms: D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods; D006801:Humans; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA