Assessment of transcript reconstruction methods for RNA-seq

Nature Methods

Volumn 10, Issue 12, 2013, Pages 1177-1184

  Steijger, Tamara ^a   Abril, Josep F ^b   Engström, Pär G ^a,h   Kokocinski, Felix ^c   Akerman, Martin ⁱ   Alioto, Tyler ^j   Ambrosini, Giovanna ^k,l   Antonarakis, Stylianos E ^m   Behr, Jonas ^n,o   Bertone, Paul ^a,f,g   Bohnert, Regina ^o   Bucher, Philipp ^k,l   Cloonan, Nicole ^p   Derrien, Thomas ^d   Djebali, Sarah ^e   Du, Jiang ^q   Dudoit, Sandrine ^r   Gerstein, Mark ^q,s   Gingeras, Thomas R ⁱ   Gonzalez, David ^d   Grimmond, Sean M ^p   Guigó, Roderic ^d,e   Habegger, Lukas ^s   Harrow, Jennifer ^c   Hubbard, Tim J ^c   Iseli, Christian ^l,t   Jean, Géraldine ^o   Kahles, André ^n,o   Lagarde, Julien ^d   Leng, Jing ^s   Lefebvre, Gregory ^k,l   Lewis, Suzanna ^u   Mortazavi, Ali ^v   Niermann, Peter ^o   Rätsch, Gunnar ^n,o   Reymond, Alexandre ^l   Ribeca, Paolo ^j   Richard, Hugues ^w   Rougemont, Jacques ^k,l   Rozowsky, Joel ^s   Sammeth, Michael ^d   Sboner, Andrea ^s   Schulz, Marcel H ^w   Searle, Steven M J ^c   Solorzano, Naryttza Diaz ^l,t   Solovyev, Victor ^x   Stanke, Mario ^y   Stevenson, Brian J ^l,t   Stockinger, Heinz ^l   Valsesia, Armand ^l,t   Weese, David ^z   White, Simon ^c   Wold, Barbara J ^aa   Wu, Jie ^i,ab   Wu, Thomas D ^ac   Zeller, Georg ^o   Zerbino, Daniel ^a   Zhang, Michael Q ⁱ   more..

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY OF BARCELONA   (Spain)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^e UNIVERSITAT POMPEU FABRA   (Spain)

^f EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^h STOCKHOLM UNIVERSITY   (Sweden)

ⁱ Cold Spring Harbor Laboratory ^*  (United States)

^j Centre Nacional d'Analisi Genomica   (Spain)

^k EPFL   (Switzerland)

^l UNIVERSITY OF LAUSANNE   (Switzerland)

^m UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

ⁿ MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^o FRIEDRICH MIESCHER LABORATORY OF THE MAX PLANCK SOCIETY   (Germany)

^p UNIVERSITY OF QUEENSLAND   (Australia)

^q Yale University   (United States)

^r UNIVERSITY OF CALIFORNIA   (United States)

^s YALE UNIVERSITY   (United States)

^t LUDWIG INSTITUTE FOR CANCER RESEARCH   (Switzerland)

^u LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^v UNIVERSITY OF CALIFORNIA   (United States)

^w MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^x UNIVERSITY OF LONDON   (United Kingdom)

^y Institute for Microbiology and Genetics   (Germany)

^z FREIE UNIVERSITÄT BERLIN   (Germany)

^aa California Institute of Technology HHMI   (United States)

^ab USA   (United States)

^ac GENENTECH INC   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; EXON; GENE EXPRESSION; GENOME; HUMAN; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSCRIPTION;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; EXONS; GENE EXPRESSION PROFILING; GENOME; HUMANS; INTRONS; RNA SPLICE SITES; RNA SPLICING; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EUKARYOTA;

EID: 84888871954     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.2714     Document Type: Article

References (36)

1. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
2. Mezlini, A.M. et al. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res. 23, 519-529 (2013).
3. Roberts, A., Pimentel, H., Trapnell, C. & Pachter, L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27, 2325-2329 (2011).
4. Li, J.J., Jiang, C.-R., Brown, J.B., Huang, H. & Bickel, P.J. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc. Natl. Acad. Sci. USA 108, 19867-19872 (2011).
5. Schulz, M.H., Zerbino, D.R., Vingron, M. & Birney, E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28, 1086-1092 (2012).
6. Grabherr, M.G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644-652 (2011).
7. Robertson, G. et al. De novo assembly and analysis of RNA-seq data. Nat. Methods 7, 909-912 (2010).
8. Guigó, R. et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 7 (suppl. 1), S2 (2006).
9. Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435-W439 (2006). (Pubitemid 44529807)
10. Slater, G.S.C. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005).
11. Schweikert, G. et al. mGene: accurate SVM-based gene finding with an application to nematode genomes. Genome Res. 19, 2133-2143 (2009).
12. Blanco, E., Parra, G. & Guigó, R. Using geneid to identify genes. Curr. Protoc. Bioinformatics 18, 4.3 (2007).
13. Sperisen, P. et al. trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res. 32, D509-D511 (2004). (Pubitemid 38081709)
14. Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008). (Pubitemid 351645072)
15. Lenhard, B., Sandelin, A. & Carninci, P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 13, 233-245 (2012).
16. Di Giammartino, D.C., Nishida, K. & Manley, J.L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853-866 (2011).
17. Tian, B., Hu, J., Zhang, H. & Lutz, C.S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33, 201-212 (2005). (Pubitemid 40276942)
18. Batut, P., Dobin, A., Plessy, C., Carninci, P. & Gingeras, T.R. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res. 23, 169-180 (2013).
19. Shepard, P.J. et al. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17, 761-772 (2011).
20. Engström, P.G. et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods doi:10.1038/nmeth.2722 (3 November 2013).
21. Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F. & Rätsch, G. RNA-Seq read alignments with PALM apper. Curr. Protoc. Bioinformatics 32, 11.6 (2010).
22. Marco-Sola, S., Sammeth, M., Guigo, R. & Ribeca, P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat. Methods 9, 1185-1188 (2012).
23. Wu, T.D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
24. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
25. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
26. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008). (Pubitemid 351911867)
27. Kulkarni, M.M. Digital multiplexed gene expression analysis using the Nano String nCounter system. Curr. Protoc. Mol. Biol. 94, 25B.10 (2011).
28. Li, B. & Dewey, C.N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).
29. Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010).
30. Bohnert, R. & Rätsch, G. rQuant.web: a tool for RNA-Seq-based transcript quantitation. Nucleic Acids Res. 38, W348-W351 (2010).
31. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
32. The modENCODE Consortium et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (2010).
33. Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
34. Graveley, B.R. et al. The developmental transcriptome of Drosophila melanogaster. Nature 471, 473-479 (2011).
35. Mortazavi, A. et al. Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res. 20, 1740-1747 (2010).
36. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).