Bioinformatics pipeline for transcriptome sequencing analysis

Methods in Molecular Biology

Volumn 1468, Issue , 2017, Pages 201-219

  Djebali, Sarah ^a   Wucher, Valentin ^a   Foissac, Sylvain ^a   Hitte, Christophe ^a   Corre, Evan ^a   Derrien, Thomas ^a  

^a NONE

Author keywords

Bioinformatics workflow; Protocols; RNA seq; Transcriptome sequencing

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BIOINFORMATICS; GENE EXPRESSION; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; K562 CELL LINE; PRIORITY JOURNAL; RNA SEQUENCE; BIOLOGY; GENE EXPRESSION PROFILING; K-562 CELL LINE; PROCEDURES; SEQUENCE ANALYSIS; WORKFLOW;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; K562 CELLS; SEQUENCE ANALYSIS, RNA; WORKFLOW;

EID: 84988706127     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-4035-6_14     Document Type: Article

References (26)

1. Wang Z, Gerstein M, Snyder M (2009) RNAseq: a revolutionary tool for transcriptomics. Nature 10:57–63
2. Djebali S, Davis CA, Merkel A et al (2012) Landscape of transcription in human cells. Nature 488:101–108 Sarah Djebali et al.
3. Dobin A, Davis CA, Schlesinger F et al (2012) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21
4. Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515
5. Li B, Ruotti V, Stewart RM et al (2010) RNAseq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493–500
6. T.E.P. Consortium, T.E.P. Consortium, O.C. Data Analysis Coordination et al (2013) An integrated encyclopedia of DNA elements in the human genome. Nature 488:57–74
7. Martens JHA, Stunnenberg HG (2013) BLUEPRINT: mapping human blood cell epigenomes. Haematologica 98:1487–1489
8. Steijger T, Abril JF, Engström PG et al (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10:1177–1184
9. Engström PG, Steijger T, Sipos B et al (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10: 1185–1191
10. Roberts A, Goff L, Pertea G et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
11. Marco-Sola S, Sammeth M, Guigó R et al (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods 9:1185–1188
12. Pertea M, Pertea GM, Antonescu CM et al (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33:290–295
13. Montgomery SB, Sammeth M, Gutierrez- Arcelus M et al (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464:773–777
14. Roberts A, Pachter L (2013) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods 10:71–73
15. Patro R, Mount SM, Kingsford C (2014) Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms. Nat Biotechnol 32:462–464
16. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512
17. Sacomoto GAT, Kielbassa J, Chikhi R et al (2012) KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics 13(Suppl 6):S5
18. Rosenbloom KR, Sloan CA, Malladi VS et al (2013) ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res 41:D56–D63
19. Harrow J, Frankish A, Gonzalez JM et al (2012) GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22:1760–1774
20. Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789
21. Pei B, Sisu C, Frankish A et al (2012) The GENCODE pseudogene resource. Genome Biol 13:R51
22. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
23. Cunningham F, Amode MR, Barrell D et al (2015) Ensembl 2015. Nucleic Acids Res 43:D662–D669
24. Knowles DG, Röder M, Merkel A et al (2013) Grape RNA-seq analysis pipeline environment. Bioinformatics 29:614–621
25. Jiang L, Schlesinger F, Davis CA et al (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Res 21:1543–1551
26. Risso D, Ngai J, Speed TP et al (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol 32:896–902