WemIQ: An accurate and robust isoform quantification method for RNA-seq data

Bioinformatics

Volumn 31, Issue 6, 2015, Pages 878-885

  Zhang, Jing ^a   Kuo, C C Jay ^a   Chen, Liang ^b  

^a University of Southern California   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; RNA;

ALGORITHM; EXON; GENE EXPRESSION PROFILING; GENETICS; HUMAN; PROCEDURES; SEQUENCE ANALYSIS; SOFTWARE; THEORETICAL MODEL;

ALGORITHMS; EXONS; GENE EXPRESSION PROFILING; HUMANS; MODELS, THEORETICAL; PROTEIN ISOFORMS; RNA; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84925245615     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu757     Document Type: Article

References (33)

1. Adiconis, X. et al. (2013) Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods, 10, 623-629.
2. Au, K.F. et al. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res., 38, 4570-4578.
3. Bohnert, R. and Ratsch, G. (2010) rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res., 38, W348-W351.
4. Brett, D. et al. (2002) Alternative splicing and genome complexity. Nat. Genet., 30, 29-30.
5. Cloonan, N. et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat. Methods, 5, 613-619.
6. Consul, P.C. (1989) Generalized Poisson Distributions: Properties and Applications. Statistics, textbooks and monographs. M. Dekker, New York.
7. Graveley, B.R. (2001) Alternative splicing: increasing diversity in the proteomic world. Trends Genet., 17, 100-107.
8. Griebel, T. et al. (2012) Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res., 40, 10073-10083.
9. Hansen, K.D. et al. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res., 38, e131.
10. Hu, Y. et al. (2014) PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Nucleic Acids Res., 42, e20.
11. Huang, Y. et al. (2013) A robust method for transcript quantification with RNA-seq data. J. Comput. Biol., 20, 167-187.
12. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
13. Li, B. and Dewey, C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
14. Li, J. et al. (2010) Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biol., 11, R50.
15. Marguerat, S. and Bahler, J. (2010) RNA-seq: from technology to biology. Cell Mol Life Sci., 67, 569-579.
16. Mezlini, A.M. et al. (2013) iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res., 23, 519-529.
17. Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628.
18. Nagalakshmi, U. et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
19. Nilsen, T.W. and Graveley, B.R. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463.
20. Pan, Q. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
21. Roberts, A. et al. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol., 12, R22.
22. Shalek, A.K. et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498, 236-240.
23. Shi, L. et al. (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
24. Srivastava, S. and Chen, L. (2010) A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res., 38, e170.
25. Steijger, T. et al. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods, 10, 1177-1184.
26. Suo, C. et al. (2014) Joint estimation of isoform expression and isoformspecific read distribution using multisample RNA-Seq data. Bioinformatics, 30, 506-513.
27. Trapnell, C. et al. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
28. Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
29. Turro, E. et al. (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol., 12, R13.
30. Wang, Z. et al. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
31. Wu, J. et al. (2011a) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27, 3010-3016.
32. Wu, Z. et al. (2011b) Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics, 27, 502-508.
33. Zheng, S. and Chen, L. (2009) A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res., 37, e75.