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Volumn 16, Issue , 2015, Pages

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

Author keywords

RNA Seq Alternative splicing transcriptome regulation workflow

Indexed keywords

RNA; TRANSCRIPTOME;

EID: 84962721515     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-16-S6-S3     Document Type: Article
Times cited : (62)

References (47)
  • 2
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews Genetics. 2009, 10 (1): 57-63. 10.1038/nrg2484.
    • (2009) Nature reviews Genetics , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 6
  • 7
    • 84899645241 scopus 로고    scopus 로고
    • FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
    • Gatto A, Torroja-Fungairino C, Mazzarotto F, Cook SA, Barton PJ, Sanchez-Cabo F, Lara-Pezzi E: FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions. Nucleic acids research. 2014, 42 (8): e71-10.1093/nar/gku166.
    • (2014) Nucleic acids research , vol.42 , Issue.8
    • Gatto, A.1    Torroja-Fungairino, C.2    Mazzarotto, F.3    Cook, S.A.4    Barton, P.J.5    Sanchez-Cabo, F.6    Lara-Pezzi, E.7
  • 10
    • 84887177848 scopus 로고    scopus 로고
    • NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
    • Boria I, Boatti L, Pesole G, Mignone F: NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. BMC Bioinformatics. 2013, 14 (Suppl 7): S10-
    • (2013) BMC Bioinformatics , vol.14 , pp. S10
    • Boria, I.1    Boatti, L.2    Pesole, G.3    Mignone, F.4
  • 16
    • 84856468953 scopus 로고    scopus 로고
    • NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
    • Patel RK, Jain M: NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PloS one. 2012, 7 (2): e30619-10.1371/journal.pone.0030619.
    • (2012) PloS one , vol.7 , Issue.2
    • Patel, R.K.1    Jain, M.2
  • 17
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology. 2013, 14 (4): R36-10.1186/gb-2013-14-4-r36.
    • (2013) Genome biology , vol.14 , Issue.4 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 20
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W: Differential expression analysis for sequence count data. Genome biology. 2010, 11 (10): R106-10.1186/gb-2010-11-10-r106.
    • (2010) Genome biology , vol.11 , Issue.10 , pp. R106
    • Anders, S.1    Huber, W.2
  • 21
    • 80054931745 scopus 로고    scopus 로고
    • SpliceTrap: a method to quantify alternative splicing under single cellular conditions
    • Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ: SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics. 2011, 27 (21): 3010-3016. 10.1093/bioinformatics/btr508.
    • (2011) Bioinformatics , vol.27 , Issue.21 , pp. 3010-3016
    • Wu, J.1    Akerman, M.2    Sun, S.3    McCombie, W.R.4    Krainer, A.R.5    Zhang, M.Q.6
  • 22
    • 80054003528 scopus 로고    scopus 로고
    • ChimeraScan: a tool for identifying chimeric transcription in sequencing data
    • Iyer MK, Chinnaiyan AM, Maher CA: ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011, 27 (20): 2903-2904. 10.1093/bioinformatics/btr467.
    • (2011) Bioinformatics , vol.27 , Issue.20 , pp. 2903-2904
    • Iyer, M.K.1    Chinnaiyan, A.M.2    Maher, C.A.3
  • 23
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009, 10 (3): R25-10.1186/gb-2009-10-3-r25.
    • (2009) Genome biology , vol.10 , Issue.3 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 24
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nature methods. 2012, 9 (4): 357-359. 10.1038/nmeth.1923.
    • (2012) Nature methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 25
    • 80051941094 scopus 로고    scopus 로고
    • Identification of novel transcripts in annotated genomes using RNA-Seq
    • Roberts A, Pimentel H, Trapnell C, Pachter L: Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011, 27 (17): 2325-2329. 10.1093/bioinformatics/btr355.
    • (2011) Bioinformatics , vol.27 , Issue.17 , pp. 2325-2329
    • Roberts, A.1    Pimentel, H.2    Trapnell, C.3    Pachter, L.4
  • 26
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • Hansen KD, Brenner SE, Dudoit S: Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic acids research. 2010, 38 (12): e131-10.1093/nar/gkq224.
    • (2010) Nucleic acids research , vol.38 , Issue.12
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 27
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic acids research. 2007, 35 (Database): D61-65. 10.1093/nar/gkl842.
    • (2007) Nucleic acids research , vol.35 , Issue.DATABASE , pp. D61-D65
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 28
    • 0033858202 scopus 로고    scopus 로고
    • Patterns of variant polyadenylation signal usage in human genes
    • Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D: Patterns of variant polyadenylation signal usage in human genes. Genome research. 2000, 10 (7): 1001-1010. 10.1101/gr.10.7.1001.
    • (2000) Genome research , vol.10 , Issue.7 , pp. 1001-1010
    • Beaudoing, E.1    Freier, S.2    Wyatt, J.R.3    Claverie, J.M.4    Gautheret, D.5
  • 29
    • 77951120000 scopus 로고    scopus 로고
    • Alternative splicing and evolution: diversification, exon definition and function
    • Keren H, Lev-Maor G, Ast G: Alternative splicing and evolution: diversification, exon definition and function. Nature reviews Genetics. 2010, 11 (5): 345-355. 10.1038/nrg2776.
    • (2010) Nature reviews Genetics , vol.11 , Issue.5 , pp. 345-355
    • Keren, H.1    Lev-Maor, G.2    Ast, G.3
  • 30
    • 84962646530 scopus 로고
    • Controlling the False Discovery Rate-a Practical and Powerful Approach to Multiple Testing
    • Benjamini Y, Hochberg Y: Controlling the False Discovery Rate-a Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc B Met. 1995, 57 (1): 289-300.
    • (1995) J Roy Stat Soc B Met , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 31
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
    • Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic acids research. 2010, 38 (6): 1767-1771. 10.1093/nar/gkp1137.
    • (2010) Nucleic acids research , vol.38 , Issue.6 , pp. 1767-1771
    • Cock, P.J.1    Fields, C.J.2    Goto, N.3    Heuer, M.L.4    Rice, P.M.5
  • 34
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL: Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & development. 2011, 25 (18): 1915-1927. 10.1101/gad.17446611.
    • (2011) Genes & development , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 37
    • 84868295073 scopus 로고    scopus 로고
    • Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms
    • Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumagi A, Kallioniemi O: Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PloS one. 2012, 7 (10): e48745-10.1371/journal.pone.0048745.
    • (2012) PloS one , vol.7 , Issue.10
    • Kangaspeska, S.1    Hultsch, S.2    Edgren, H.3    Nicorici, D.4    Murumagi, A.5    Kallioniemi, O.6
  • 43
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010, 26 (1): 139-140. 10.1093/bioinformatics/btp616.
    • (2010) Bioinformatics , vol.26 , Issue.1 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 45
    • 77955298482 scopus 로고    scopus 로고
    • baySeq: empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle TJ, Kelly KA: baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC bioinformatics. 2010, 11: 422-10.1186/1471-2105-11-422.
    • (2010) BMC bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 47
    • 84867680338 scopus 로고    scopus 로고
    • PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
    • Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P: PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC bioinformatics. 2012, 13 (Suppl 5): S2-10.1186/1471-2105-13-S5-S2.
    • (2012) BMC bioinformatics , vol.13 , pp. S2
    • Pirola, Y.1    Rizzi, R.2    Picardi, E.3    Pesole, G.4    Della Vedova, G.5    Bonizzoni, P.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.