title: Modeling non-uniformity in short-read rates in RNA-Seq data.
abstract: After mapping, RNA-Seq data can be summarized by a sequence of read counts commonly modeled as Poisson variables with constant rates along each transcript, which actually fit data poorly. We suggest using variable rates for different positions, and propose two models to predict these rates based on local sequences. These models explain more than 50% of the variations and can lead to improved estimates of gene and isoform expressions for both Illumina and Applied Biosystems data.
authors.affiliation: Department of Statistics, Stanford University, Sequoia Hall, 390 Serra Mall, Stanford, CA 94305, USA. junli07@stanford.edu
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
mesh_terms: D000818:Animals; D001057:Apolipoproteins E / Q000235:genetics; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D004622:Embryo, Mammalian / Q000378:metabolism; D005091:Exons / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D016014:Linear Models; D051379:Mice; D008957:Models, Genetic; D016012:Poisson Distribution; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D018709:Statistics, Nonparametric
chemical_list: D001057:Apolipoproteins E; D020033:Protein Isoforms; D012313:RNA
references.citation: Bioinformatics. 2008 Dec 1;24(23):2776-7
references.pmid: 18842598
references.citation: Biotechniques. 2008 Jul;45(1):81-94
references.pmid: 18611170
references.citation: Nucleic Acids Res. 2008 Sep;36(16):e105
references.pmid: 18660515
references.citation: Nucleic Acids Res. 2007;35(15):e99
references.pmid: 17686789
references.citation: Nucleic Acids Res. 2003 Feb 15;31(4):e15
references.pmid: 12582260
references.citation: Cell. 2008 May 2;133(3):523-36
references.pmid: 18423832
references.citation: Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Jul;68(1 Pt 1):011906
references.pmid: 12935175
references.citation: Nature. 2008 Jun 26;453(7199):1239-43
references.pmid: 18488015
references.citation: Mol Cell. 2004 Dec 22;16(6):929-41
references.pmid: 15610736
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: BMC Bioinformatics. 2008 Oct 23;9:453
references.pmid: 18947421
references.citation: Nucleic Acids Res. 2010 Jul;38(12):e131
references.pmid: 20395217
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62
references.pmid: 16895995
references.citation: Bioinformatics. 2008 Dec 15;24(24):2887-93
references.pmid: 18984598
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850
references.citation: BMC Bioinformatics. 2006 Jun 02;7:276
references.pmid: 16749918
references.citation: Nat Genet. 2008 Dec;40(12):1413-5
references.pmid: 18978789
references.citation: Nat Biotechnol. 2008 Nov;26(11):1293-300
references.pmid: 18978777
references.citation: Bioinformatics. 2009 Apr 15;25(8):1026-32
references.pmid: 19244387
references.citation: Nat Methods. 2008 Jul;5(7):613-9
references.pmid: 18516046
references.citation: Bioinformatics. 2008 Oct 15;24(20):2395-6
references.pmid: 18697769
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Genome Res. 2008 Jun;18(6):839-46
references.pmid: 18519653
references.citation: Genome Biol. 2007;8(8):R178
references.pmid: 17727723