A comparative study of RNA-seq analysis strategies

作者: J. Janes , F. Hu , A. Lewin , E. Turro

DOI: 10.1093/BIB/BBV007

关键词:

摘要: This work was supported by the Wellcome Trust (WT097679); Cambridge Biomedical Research Centre; Cancer UK (C14303/A10825) and Medical Council (G1002319).

参考文章(15)
Massingham T, Goldman N, Slodkowicz G, Sipos B, Realistic simulations reveal extensive sample-specificity of RNA-seq biases arXiv: Genomics. ,(2013)
Mitchell Guttman, Manuel Garber, Joshua Z Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J Koziol, Andreas Gnirke, Chad Nusbaum, John L Rinn, Eric S Lander, Aviv Regev, Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs Nature Biotechnology. ,vol. 28, pp. 503- 510 ,(2010) , 10.1038/NBT.1633
K. D. Pruitt, T. Tatusova, G. R. Brown, D. R. Maglott, NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy Nucleic Acids Research. ,vol. 40, pp. 130- 135 ,(2012) , 10.1093/NAR/GKR1079
Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William Mclaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y Amy Tang, Stephen Trevanion, Albert Vilella, Jan Vogel, Simon White, Steven P Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M Fernández-Suarez, Javier Herrero, Tim JP Hubbard, Anne Parker, Glenn Proctor, James Smith, Stephen MJ Searle, Paul Flicek, Bronwen L Aken, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew Jenkinson, None, Ensembl’s 10th year Nucleic Acids Research. ,vol. 38, pp. 557- 562 ,(2010) , 10.1093/NAR/GKP972
Thasso Griebel, Benedikt Zacher, Paolo Ribeca, Emanuele Raineri, Vincent Lacroix, Roderic Guigó, Michael Sammeth, Modelling and simulating generic RNA-Seq experiments with the flux simulator Nucleic Acids Research. ,vol. 40, pp. 10073- 10083 ,(2012) , 10.1093/NAR/GKS666
Manuel Garber, Manfred G Grabherr, Mitchell Guttman, Cole Trapnell, Computational methods for transcriptome annotation and quantification using RNA-seq Nature Methods. ,vol. 8, pp. 469- 477 ,(2011) , 10.1038/NMETH.1613
A. Roberts, H. Pimentel, C. Trapnell, L. Pachter, Identification of novel transcripts in annotated genomes using RNA-Seq Bioinformatics. ,vol. 27, pp. 2325- 2329 ,(2011) , 10.1093/BIOINFORMATICS/BTR355
Gordon Robertson, Jacqueline Schein, Readman Chiu, Richard Corbett, Matthew Field, Shaun D Jackman, Karen Mungall, Sam Lee, Hisanaga Mark Okada, Jenny Q Qian, Malachi Griffith, Anthony Raymond, Nina Thiessen, Timothee Cezard, Yaron S Butterfield, Richard Newsome, Simon K Chan, Rong She, Richard Varhol, Baljit Kamoh, Anna-Liisa Prabhu, Angela Tam, YongJun Zhao, Richard A Moore, Martin Hirst, Marco A Marra, Steven J M Jones, Pamela A Hoodless, Inanc Birol, De novo assembly and analysis of RNA-seq data Nature Methods. ,vol. 7, pp. 909- 912 ,(2010) , 10.1038/NMETH.1517
Tamara Steijger, Josep F Abril, Pär G Engström, Felix Kokocinski, Martin Akerman, Tyler Alioto, Giovanna Ambrosini, Stylianos E Antonarakis, Jonas Behr, Paul Bertone, Regina Bohnert, Philipp Bucher, Nicole Cloonan, Thomas Derrien, Sarah Djebali, Jiang Du, Sandrine Dudoit, Mark Gerstein, Thomas R Gingeras, David Gonzalez, Sean M Grimmond, Roderic Guigó, Lukas Habegger, Jennifer Harrow, Tim J Hubbard, Christian Iseli, Géraldine Jean, André Kahles, Julien Lagarde, Jing Leng, Gregory Lefebvre, Suzanna Lewis, Ali Mortazavi, Peter Niermann, Gunnar Rätsch, Alexandre Reymond, Paolo Ribeca, Hugues Richard, Jacques Rougemont, Joel Rozowsky, Michael Sammeth, Andrea Sboner, Marcel H Schulz, Steven MJ Searle, Naryttza Diaz Solorzano, Victor Solovyev, Mario Stanke, Brian J Stevenson, Heinz Stockinger, Armand Valsesia, David Weese, Simon White, Barbara J Wold, Jie Wu, Thomas D Wu, Georg Zeller, Daniel Zerbino, Michael Q Zhang, RGASP Consortium, Assessment of transcript reconstruction methods for RNA-seq Nature Methods. ,vol. 10, pp. 1177- 1184 ,(2013) , 10.1038/NMETH.2714
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman, Aviv Regev, Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. ,vol. 29, pp. 644- 652 ,(2011) , 10.1038/NBT.1883