Analysis of RNA-seq data using TopHat and cufflinks

Methods in Molecular Biology

Volumn 1374, Issue , 2016, Pages 339-361

  Ghosh, Sreya ^a   Chan, Chon Kit Kenneth ^a  

^a NONE

Author keywords

Bowtie; Cuffcompare; Cuffdiff; Cufflinks; Cuffmerge; CummeRbund; Differential gene expression; RNA seq; TopHat; Transcriptome assembly

Indexed keywords

RNA; TRANSCRIPTOME;

ALGORITHM; ALTERNATIVE RNA SPLICING; ARABIDOPSIS THALIANA; COMPUTER PROGRAM; GENE EXPRESSION; GENOME; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; NONHUMAN; RNA SEQUENCE; SEQUENCE ALIGNMENT; TRANSCRIPTION REGULATION; WORKFLOW; BIOLOGY; GENE EXPRESSION PROFILING; GENOMICS; PROCEDURES; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENOMICS; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 84946031490     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3167-5_18     Document Type: Chapter

References (39)

1. Ozsolak F, Milos PM (2011) RNA sequencing: advances, challenges and opportunities. Nat Rev Genet 12(2):87–98. doi: 10.1038/nrg2934
2. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11(1):31–46. doi: 10.1038/nrg2626
3. Mardis ER (2008) The impact of nextgeneration sequencing technology on genetics. Trends Genet 24(3):133–141. doi: 10.1016/j.tig.2007.12.007
4. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18(9):1509–1517. doi: 10.1101/gr.079558.108
5. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, Bowers J, Jarosz M, Milos PM (2009) Direct RNA sequencing. Nature 461(7265):814–818. doi: 10.1038/nature08390
6. Roy SW, Irimia M (2008) When good transcripts go bad: artifactual RT-PCR ‘splicing’ and genome analysis. BioEssays 30(6):601–605. doi: 10.1002/bies.20749
7. Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8(6):469–477. doi: 10.1038/nmeth.1613
8. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515. doi: 10.1038/nbt.1621
9. Wang Z, Gerstein M, Snyder M (2009) RNASeq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1):57–63. doi: 10.1038/nrg2484
10. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467–470
11. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 93(20):10614–10619
12. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100(26):15776–15781. doi: 10.1073/pnas.2136655100
13. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D, Imamura K, Kai C, Harbers M, Hayashizaki Y, Carninci P (2006) CAGE: cap analysis of gene expression. Nat Methods 3(3):211–222. doi: 10.1038/nmeth0306-211
14. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270(5235):484–487
15. Reinartz J, Bruyns E, Lin JZ, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R (2002) Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Funct Genomic Proteomic 1(1):95–104
16. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18(6):630–634. doi: 10.1038/76469
17. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. doi: 10.1038/nmeth.1226
18. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12:317. doi: 10.1186/1471-2164-12-317
19. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25. doi: 10.1186/gb-2009-10-3-r25
20. Li H, Durbin R (2010) Fast and accurate longread alignment with Burrows-Wheeler transform. Bioinformatics 26(5):589–595. doi: 10.1093/bioinformatics/btp698
21. Simpson JT, Durbin R (2010) Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26(12):i367–i373. doi: 10.1093/bioinformatics/btq217
22. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111. doi: 10.1093/bioinformatics/btp120
23. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562–578. doi: 10.1038/nprot.2012.016
24. Goff L, Trapnell C, Kelley D, Guide PRSCU, biocViews Clustering D, DataRepresentation D, GeneExpression I, MultipleComparison Q, RNASeq R, since BioC IB (2012) Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. R package version 2 (1)
25. Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86. doi: 10.1186/gb-2010-11-8-r86
26. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966–1967. doi: 10.1093/bioinformatics/btp336
27. Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21(6):936–939. doi: 10.1101/gr.111120.110
28. Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38(18), e178. doi: 10.1093/nar/gkq622
29. Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26(7):873–881. doi: 10.1093/bioinformatics/btq057
30. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5):503–510. doi: 10.1038/nbt.1633
31. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829. doi: 10.1101/gr.074492.107
32. Lee S, Seo CH, Lim B, Yang JO, Oh J, Kim M, Lee S, Lee B, Kang C, Lee S (2011) Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. Nucleic Acids Res 39(2):e9. doi: 10.1093/nar/gkq1015
33. Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26(1):136–138. doi: 10.1093/bioinformatics/btp612
34. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106. doi: 10.1186/gb-2010-11-10-r106
35. Twine NA, Janitz K, Wilkins MR, Janitz M (2011) Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease. PLoS One 6(1), e16266
36. Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutierrez RA (2013) Integrated RNA-seq and sRNA-seq analysis identifies novel nitrateresponsive genes in Arabidopsis thaliana roots. BMC Genomics 14:701. doi: 10.1186/1471-2164-14-701
37. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079. doi: 10.1093/bioinformatics/btp352
38. Alexandrov NN, Troukhan ME, Brover VV, Tatarinova T, Flavell RB, Feldmann KA (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60(1):69–85. doi: 10.1007/s11103-005-2564-9
39. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20(1):45–58. doi: 10.1101/gr.093302.109