De novo assembly and analysis of RNA-seq data

作者: Gordon Robertson , Jacqueline Schein , Readman Chiu , Richard Corbett , Matthew Field

DOI: 10.1038/NMETH.1517

关键词:

摘要: … assembly practical for characterizing annotated and new transcript structures, we anticipated that it would be necessary to assemble … a method and pipeline for assembly and analysis of …

参考文章(31)
Guy Slater, Ewan Birney, Automated generation of heuristics for biological sequence comparison BMC Bioinformatics. ,vol. 6, pp. 31- 31 ,(2005) , 10.1186/1471-2105-6-31
J. T. Simpson, K. Wong, S. D. Jackman, J. E. Schein, S. J.M. Jones, I. Birol, ABySS: A parallel assembler for short read sequence data Genome Research. ,vol. 19, pp. 1117- 1123 ,(2009) , 10.1101/GR.089532.108
Shirley Pepke, Barbara Wold, Ali Mortazavi, Computation for ChIP-seq and RNA-seq studies Nature Methods. ,vol. 6, ,(2009) , 10.1038/NMETH.1371
U. Nagalakshmi, Z. Wang, K. Waern, C. Shou, D. Raha, M. Gerstein, M. Snyder, The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing Science. ,vol. 320, pp. 1344- 1349 ,(2008) , 10.1126/SCIENCE.1158441
Fabian Birzele, Jochen Schaub, Werner Rust, Christoph Clemens, Patrick Baum, Hitto Kaufmann, Andreas Weith, Torsten W. Schulz, Tobias Hildebrandt, Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing Nucleic Acids Research. ,vol. 38, pp. 3999- 4010 ,(2010) , 10.1093/NAR/GKQ116
Eugene Melamud, John Moult, Stochastic noise in splicing machinery Nucleic Acids Research. ,vol. 37, pp. 4873- 4886 ,(2009) , 10.1093/NAR/GKP471
Cole Trapnell, Steven L Salzberg, How to map billions of short reads onto genomes. Nature Biotechnology. ,vol. 27, pp. 455- 457 ,(2009) , 10.1038/NBT0509-455
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
Shaun D Jackman, İnanç Birol, Assembling genomes using short-read sequencing technology Genome Biology. ,vol. 11, pp. 202- 202 ,(2010) , 10.1186/GB-2010-11-1-202
Jun Li, Hui Jiang, Wing Wong, Modeling non-uniformity in short-read rates in RNA-Seq data. Genome Biology. ,vol. 11, pp. 1- 11 ,(2010) , 10.1186/GB-2010-11-5-R50