Methods to study splicing from high-throughput RNA sequencing data

Methods in Molecular Biology

Volumn 1126, Issue , 2014, Pages 357-397

  Alamancos, Gael P ^a   Agirre, Eneritz ^a   Eyras, Eduardo ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

Alternative splicing; Isoform; Quantification; Reconstruction; RNA Seq; Splicing

Indexed keywords

RNA; TRANSCRIPTOME;

ARTICLE; GENOME; HIGH THROUGHPUT SEQUENCING; PRIORITY JOURNAL; RNA SPLICING;

ALGORITHMS; EXONS; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR BIOLOGY; RNA; RNA SPLICE SITES; RNA SPLICING; SEQUENCE ANALYSIS, RNA;

EID: 84934439290     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-980-2_26     Document Type: Article

References (143)

1. Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 489(7414):101-108
2. Wang ET, Sandberg R, Luo S et al (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456(7221):470-476
3. Pan Q, Shai O, Lee LJ et al (2008) Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat Genet 40(12): 1413-1415
4. Chen L (2011) Statistical and computational studies on alternative splicing. In: Horng- Shing Lu H et al (eds) Handbook of statistical bioinformatics. Springer, New York. doi: 10.1007/978-3-642-16345-6-2
5. Pachter L (2011) Models for transcript quantifi cation from RNA-Seq. arXiv:1104.3889v2 (http://arxiv.org/abs/1104.3889)
6. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105-1111
7. Huang S, Zhang J, Li R et al (2011) SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data. Front Genet 2(July):46
8. Zhang Y, Lameijer EW, 't Hoen PA et al (2012) PASSion: a pattern growth algorithmbased pipeline for splice junction detection in paired-end RNA-Seq data. Bioinformatics 28(4):479-486
9. Wang K, Singh D, Zeng Z et al (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res 38(18):e178
10. Au KF, Jiang H, Lin L et al (2010) Detection of splice junctions from paired-end RNA seq data by SpliceMap. Nucleic Acids Res 38(14):4570-4578
11. Dimon MT, Sorber K, DeRisi JL (2010) HMMSplicer: a tool for effi cient and sensitive discovery of known and novel splice junctions in RNA-Seq data. PloS one 5(11):e13875
12. Li Y, Li-Byarlay H, Burns P et al (2013) TrueSight: a new algorithm for splice junction detection using RNA-seq. Nucleic Acids Res 41(4):e51
13. Marco-Sola S, Sammeth M, Guigó R et al (2012) The GEM mapper: fast, accurate and versatile alignment by fi ltration. Nat Methods 9(12):1185-1188
14. Ameur A, Wetterbom A, Feuk L et al (2010) Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol 11(3):R34
15. Bryant DW, Shen R, Priest HD et al (2010) Supersplat- spliced RNA-seq alignment. Bioinformatics 26(12):1500-1505
16. Wang L, Wang X, Wang X et al (2011) Observations on novel splice junctions from RNA sequencing data. Biochem Biophys Res Commun 409(2):299-303
17. Lou SK, Ni B, Lo LY et al (2011) ABMapper: a suffi x array-based tool for multi-location searching and splice-junction mapping. Bioinformatics 27(3):421-422
18. Bao H, Xiong Y, Guo H et al (2009) MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics 10(Suppl 3):S13
19. Dobin A, Davis CA, Schlesinger F et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15-21
20. Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26(7):873-881
21. De Bona F, Ossowski S, Schneeberger K et al (2008) Optimal spliced alignments of short sequence reads. Bioinformatics 24(16): i174-i180
22. Jean G, Kahles A, Sreedharan VT et al. (2010) RNA-Seq read alignments with PALMapper. Curr Protoc Bioinformat Chapter 11:Unit 11.6
23. Philippe N, Salson M, Commes T et al (2013) CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biol 14(3):R30
24. Wu J, Anczuków O, Krainer AR et al (2013) OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucl Acids Res 41(10):5149-5163
25. Liao Y, Smyth GK, Shi W (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41(10):e108
26. Hu J, Ge H, Newman M, Liu K (2012) OSA: a fast and accurate alignment tool for RNA- Seq. Bioinformatics 28(14):1933-1934
27. Wood DL, Xu Q, Pearson JV et al (2011) X-MATE: a fl exible system for mapping short read data. Bioinformatics 27(4):580-581
28. Chen LY, Wei KC, Huang AC et al (2012) RNASEQR - a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res 40(6):e42
29. Labaj PP, Linggi BE, Wiley HS et al (2012) Improving RNA-Seq Precision with MapAl. Front Genet 3:28
30. Xu G, Deng N, Zhao Z et al (2011) SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol Med 6(1):2
31. Kim H, Bi Y, Pal S et al (2011) IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-seq data. BMC Bioinforma 12:305
32. Grant GR, Farkas MH, Pizarro AD et al (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unifi ed mapper (RUM). Bioinformatics 27(18): 2518-2528
33. Ryan MC, Cleland J, Kim R et al (2012) SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts. Bioinformatics 28(18):2385-2387
34. Tang S, Riva A (2013) PASTA: splice junction identifi cation from RNA-Sequencing data. BMC Bioinforma 14(1):116
35. Bonfert T, Csaba G, Zimmer R et al (2012) A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinforma 13(Suppl 6):S9
36. Wang L, Xi Y, Yu J et al (2010) A statistical method for the detection of alternative splicing using RNA-seq. PLoS one 5(1):e8529
37. Wu J, Akerman M, Sun S et al (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics 27:3010-3016
38. Katz Y, Wang ET, Airoldi EM et al (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7(12):1009-1015
39. Griffi th M, Griffi th OL, Mwenifumbo J et al (2010) Alternative expression analysis by RNA sequencing. Nat Methods 7(10):843-847
40. Richard H, Schulz MH, Sultan M et al (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucl Acids Res 38(10):e112
41. Mortazavi A, Williams BA, Mccue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):1-8
42. Jiang H, Wong WH (2009) Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 25(8):1026-1032
43. Bohnert R, Behr J, Rätsch G (2009) Transcript quantifi cation with RNA-Seq data. BMC Bioinforma 10(Suppl 13):P5
44. Montgomery SB, Sammeth M, Gutierrez- Arcelus M et al (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464(7289): 773-777
45. Du J, Leng J, Habegger L et al (2012) IQSeq: integrated isoform quantifi cation analysis based on next-generation sequencing. PLoS One 7(1):e29175
46. Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and quantifi cation by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511-515
47. Rossell D, Attolini CSO, Kroiss M et al. (2012) Quantifying alternative splicing from paired-end RNA-sequencing data. COBRA Preprint Series. Working Paper 97 http:// biostats.bepress.com/cobra/art97
48. Li W, Jiang T (2012) Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads. Bioinformatics 28(22):2914-2921
49. Li W, Feng J, Jiang T (2011) IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J Comput Biol 18(11):1693-1707
50. Feng J, Li W, Jiang T (2010) Inference of isoforms from short sequence reads. In: Berger B (ed) Research in computational molecular biology, lecture notes in computer science, vol 6044. Springer, Heidelberg, pp 138-157
51. Li JJ, Jiang CR, Brown JB et al (2011) Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. PNAS 108(50):19867-19872
52. Roberts A, Pimentel H, Trapnell C et al (2011) Identifi cation of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27(17):2325-2329
53. Mangul S, Caciula A, Glebova O et al (2012) Improved transcriptome quantifi cation and reconstruction from RNA-Seq reads using partial annotations. Silico Biol 11(5): 251-261
54. Mezlini AM, Smith EJ, Fiume M et al (2013) iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res 23(3):519-529
55. Li B, Dewey CN (2011) RSEM: accurate transcript quantifi cation from RNA-Seq data with or without a reference genome. BMC Bioinforma 12:323
56. Nicolae N, Mangul S, Mandoiu I et al (2011) Estimation of alternative splicing isoform frequencies from RNA-seq data. Algorithms Mol Biol 6:9
57. Lee S, Seo CH, Lim B et al (2011) Accurate quantifi cation of transcriptome from RNAseq data by effective length normalization. Nucleic Acids Res 39(2):e9
58. Glaus P, Honkela A, Rattray M (2012) Identifying differentially expressed transcripts from RNA-seq data with biological variation. Bioinformatics 28(13):1721-1728
59. Turro E, Su SY, Gonçalves  et al (2011) Haplotype and isoform specifi c expression estimation using multi-mapping RNA-seq reads. Genome Biol 12(2):R13
60. Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10(1): 71-73
61. Denoeud F, Aury JM, Da Silva C et al (2008) Annotating genomes with massive-scale RNA sequencing. Genome Biol 9(12):R175
62. Zhao Z, Nguyen T, Deng N et al. (2011) SPATA: a seeding and patching algorithm for de novo transcriptome assembly. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshop (IEEE BIBMW'11) pp. 26-33
63. Filichkin S, Priest H, Givan S et al (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20(1): 45-58
64. Guttman M, Garber M, Levin JZ et al (2010) Ab initio reconstruction of cell type-specifi c transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5):503-510
65. Hiller D, Wong WH (2012) Simultaneous isoform discovery and quantifi cation from RNA-Seq. Stat Biosci 5(1):100-118
66. Xia Z, Wen J, Chang CC et al (2011) NSMAP: a method for spliced isoforms identifi cation and quantifi cation from RNA-Seq. BMC Bioinforma 12:162
67. Rogers MF, Thomas J, Reddy AS et al (2012) SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol 13(1):R4
68. Seok J, Xu W, Jiang H et al (2012) Knowledgebased reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. PLoS ONE 7(2):e31440
69. Behr J, Bohnert R, Zeller G et al (2010) Next generation genome annotation with mGene. ngs. BMC Bioinforma 11(Suppl 10):O8
70. Stanke M, Schöffmann O, Morgenstern B et al (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinforma 7:62
71. Howe KL, Chothia T, Durbin R (2002) GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res 12(9):1418-1427
72. Allen JE, Salzberg SL (2005) JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics 21(18): 3596-3603
73. Haas BJ, Salzberg SL, Zhu W et al (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol 9(1):R7
74. Liu Q, Mackey AJ, Roos DS et al (2008) Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics 24(5):597-605
75. Martin J, Bruno VM, Fang Z et al (2010) Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNASeq reads. BMC Genomics 11:663
76. Surget-Groba Y, Montoya-Burgos J (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20(10):1432-1440
77. Schulz MH, Zerbino DR, Vingron M et al (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 28(8):1086-1092
78. Xie Y, Wu G, Tang J et al. (2013) SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. arXiv:1305.6760 [q-bio.GN] (http://arxiv. org/abs/1305.6760)
79. Robertson G, Schein J, Chiu R et al (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7(11):909-912
80. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644-652
81. Sacomoto GA, Kielbassa J, Chikhi R et al (2012) KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinforma 13(Suppl 6):S5
82. Anders S, Reyes A, Huber W (2012) Detecting differential usage of exons from RNA-seq data. Genome Res 22(10): 2008-2017
83. Wang W, Qin Z, Feng Z et al (2013) Identifying differentially spliced genes from two groups of RNA-seq samples. Gene 518(1):164-170
84. Srivastava S, Chen L (2010) A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res 38(17):e170
85. Shen S, Park JW, Huang J et al (2012) MATS: a Bayesian framework for fl exible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Res 40(8):e61
86. Brooks AN, Yang L, Duff MO et al (2011) Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 21(2):193-202
87. Seok J, Xu W, Gao H et al (2012) JETTA: junction and exon toolkits for transcriptome analysis. Bioinformatics 28(9):1274-1275
88. Aschoff M, Hotz-Wagenblatt A, Glatting KH et al (2013) SplicingCompass: differential splicing detection using RNA-Seq data. Bioinformatics 29(9):1141-1148
89. Hu Y, Huang Y, Du Y et al (2013) DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Nucleic Acids Res 41(2):e39
90. Singh D, Orellana CF, Hu Y et al (2011) FDM: a graph-based statistical method to detect differential transcription using RNAseq data. Bioinformatics 27(19):2633-2640
91. Drewe P, Stegle O, Hartmann L et al (2013) Accurate detection of differential RNA processing. Nucl Acids Res 41(10):5189-5198
92. Zheng S, Chen L (2009) A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res 37(10):e75
93. Trapnell C, Hendrickson DG, Sauvageau M et al (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31(1):46-53
94. Leng N, Dawson JA, Thomson JA et al (2013) EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29(8):1035-1043
95. Fiume M, Williams V, Brook A et al (2010) Savant: genome browser for high-throughput sequencing data. Bioinformatics 26(16): 1938-1944
96. Liu Q, Chen C, Shen E et al (2012) Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer. Genomics 99(3):178-182
97. Slater GS, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinforma 6:31
98. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4):656-664
99. Wu TD, Watanabe CK (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21(9):1859-1875
100. Fonseca NA, Rung J, Brazma A et al (2012) Tools for mapping high-throughput sequencing data. Bioinformatics 28(24):3169-3177
101. Garber M, Grabherr MG, Guttman M et al (2011) Computational methods for transcriptome annotation and quantifi cation using RNA-seq. Nat Methods 8(6):469-477
102. Schneeberger K, Hagmann J, Ossowski S et al (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biol 10(9):R98
103. Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory effi cient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25
104. Clark TA, Sugnet CW, Ares M Jr (2002) Genome wide analysis of mRNA processing in yeast using splicing-specifi c microarrays. Science 296(5569):907-910
105. Sultan M, Schulz MH, Richard H et al (2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321(5891):956-960
106. Cloonan N, Forrest ARR, Kolle G et al (2008) Stem cell transcriptome profi ling via massive scale mRNA sequencing. Nat Methods 5(7):613-619
107. Cloonan N, Xu Q, Faulkner GJ et al (2009) RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data. Bioinformatics 25(19):2615-2616
108. Tang F, Barbacioru C, Wang Y et al (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6(5):377-382
109. Chen L (2012) Statistical and computational methods for high-throughput sequencing data analysis of alternative splicing. Stat Biosci 5(1):138-155
110. Venables JP, Klinck R, Bramard A et al (2008) Identifi cation of alternative splicing markers for breast cancer. Cancer Res 68(22): 9525-9531
111. Li R, Yu C, Li Y et al (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15):1966-1967
112. Deng N, Puetter A, Zhang K et al (2011) Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res 39(9):e61
113. Nguyen TC, Deng N, Zhu D (2013) SASeq: a selective and adaptive shrinkage approach to detect and quantify active transcripts using RNA-Seq. arXiv:1208.3619 v2 [q-bio.QM] (http://arxiv.org/abs/1208.3619v2)
114. Heber S, Alekseyev M, Sze SH et al (2002) Splicing graphs and EST assembly problem. Bioinformatics 18(Suppl 1):S181-S188
115. Haas BJ, Delcher AL, Mount SM et al (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31:5654-5666
116. Xing Y, Resch A, Lee C (2004) The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures. Genome Res 14(3):426-441
117. Xing Y, Yu T, Wu YN et al (2006) An expectation- maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 34(10):3150-3160
118. Nagaraj SH, Gasser RB, Ranganathan S (2007) A hitchhiker's guide to expressed sequence tag (EST) analysis. Brief Bioinform 8(1):6-21
119. Salzman J, Jiang H, Wong WH (2011) Statistical modeling of RNA-Seq data. Stat Sci 26(1):62-83
120. Li B, Ruotti V, Stewart R et al (2010) RNASeq gene expression estimation with read mapping uncertainty. Bioinformatics 26(4):493-500
121. Sonnenburg S, Schweikert G, Philips P et al (2007) Accurate splice site prediction using support vector machines. BMC Bioinforma 8(Suppl 10):S7
122. Stanke M, Keller O, Gunduz I et al (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34(Web Server issue):W435-W439
123. Guigó R, Flicek P, Abril JF et al (2006) EGASP: the human ENCODE genome annotation assessment project. Genome Biol 7(Suppl 1):S2.1-31
124. Pontius JU, Wagner L, Schuler GD (2003) UniGene: a unifi ed view of the transcriptome. In: The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ books/NBK21083/
125. Zhao QY, Wang Y, Kong YM et al (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinforma 12(Suppl 14):S2
126. Jackson B, Schnable P, Aluru S (2009) Parallel short sequence assembly of transcriptomes. BMC Bioinforma 10(Suppl 1):S14
127. Vijay N, Poelstra JW, Künstner A et al (2013) Challenges and strategies in transcriptome assembly and differential gene expression quantifi cation. A comprehensive in silico assessment of RNA-seq experiments. Mol Ecol 22(3):620-634
128. Stegle O, Drewe P, Bohnert R et al (2010) Statistical tests for detecting differential rna- transcript expression from read counts. Nat Preced. doi: 10.1038/npre.2010.4437.1
129. Kakaradov B, Xiong HY, Lee LJ et al (2012) Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. BMC Bioinforma 13(Suppl 6):S11
130. Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24(20):2395-2396
131. Borgwardt KM, Gretton A, Rasch MJ et al (2006) Integrating structured biological data by Kernel Maximum Mean Discrepancy. Bioinformatics 22(14):e49-e57
132. Hansen KD, Wu Z, Irizarry RA et al (2011) Sequencing technology does not eliminate biological variability. Nat Biotechnol 29: 572-573
133. Oshlack A, Robinson MD, Young MD (2010) From RNA-seq reads to differential expression results. Genome Biol 11(12):220. doi: 10.1186/gb-2010-11-12-220
134. Bhasi A, Philip P, Sreedharan VT et al (2009) AspAlt: A tool for inter-database, inter- genomic and user-specifi c comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes. Genomics 94(1):48-54
135. Martelli PL, D'Antonio M, Bonizzoni P et al (2011) ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res 39(Database issue):D80-D85
136. Karolchik D, Hinrichs AS, Kent WJ (2012) The UCSC Genome Browser. Curr Protoc Bioinformatics Chapter 1:Unit1.4
137. Donlin MJ. (2009) Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics, Chapter 9:Unit 9.9
138. Lee E, Harris N, Gibson M et al (2009) Apollo: a community resource for genome annotation editing. Bioinformatics 25: 1836-1837
139. Pyrkosz AB, Cheng H, Brown CT. (2013) RNA-Seq Mapping Errors When Using Incomplete Reference Transcriptomes of Vertebrates. arXiv:1303.2411 [q-bio.GN] (http://arxiv.org/abs/1303.2411)
140. Birzele F, Schaub J, Rust W et al (2010) Into the unknown: expression profi ling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res 38(12):3999-4010
141. MacManes MD, Eisen MB (2013) Improving transcriptome assembly through error correction of high-throughput sequence reads. arXiv:1304.0817 [q-bio.GN] (http://arxiv. org/abs/1304.0817) (3/April/2013)
142. Eyras E, Caccamo M, Curwen V et al (2004) ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res 14(5):976-987
143. Lovén J, Orlando DA, Sigova AA et al (2012) Revisiting global gene expression analysis. Cell 151(3):476-482