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Volumn 5, Issue , 2016, Pages

SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; DNA; GENOMIC DNA; RNA;

EID: 85011005476     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/F1000RESEARCH.9037.2     Document Type: Article
Times cited : (132)

References (26)
  • 1
    • 84890023970 scopus 로고    scopus 로고
    • Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
    • Selvaraj S, Dixon JR, Bansal V, et al.: Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 2013; 31(12): 1111-1118.
    • (2013) Nat Biotechnol , vol.31 , Issue.12 , pp. 1111-1118
    • Selvaraj, S.1    Dixon, J.R.2    Bansal, V.3
  • 2
    • 84929015299 scopus 로고    scopus 로고
    • Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome
    • Rivas MA, Pirinen M, Conrad DF, et al.: Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science. 2015; 348(6235): 666-669.
    • (2015) Science , vol.348 , Issue.6235 , pp. 666-669
    • Rivas, M.A.1    Pirinen, M.2    Conrad, D.F.3
  • 3
    • 70349910898 scopus 로고    scopus 로고
    • Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    • Degner JF, Marioni JC, Pai AA, et al.: Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics. 2009; 25(24): 3207-3212.
    • (2009) Bioinformatics , vol.25 , Issue.24 , pp. 3207-3212
    • Degner, J.F.1    Marioni, J.C.2    Pai, A.A.3
  • 4
    • 84925842188 scopus 로고    scopus 로고
    • Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
    • Crowley JJ, Zhabotynsky V, Sun W, et al.: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015; 47(4): 353-360.
    • (2015) Nat Genet , vol.47 , Issue.4 , pp. 353-360
    • Crowley, J.J.1    Zhabotynsky, V.2    Sun, W.3
  • 5
    • 80051489977 scopus 로고    scopus 로고
    • AlleleSeq: analysis of allele-specific expression and binding in a network framework
    • Rozowsky J, Abyzov A, Wang J, et al.: AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011; 7(1): 522.
    • (2011) Mol Syst Biol , vol.7 , Issue.1 , pp. 522
    • Rozowsky, J.1    Abyzov, A.2    Wang, J.3
  • 6
    • 84857331867 scopus 로고    scopus 로고
    • Base-resolution analyses of sequence and parentof-origin dependent DNA methylation in the mouse genome
    • Xie W, Barr CL, Kim A, et al.: Base-resolution analyses of sequence and parentof-origin dependent DNA methylation in the mouse genome. Cell. 2012; 148(4): 816-831.
    • (2012) Cell , vol.148 , Issue.4 , pp. 816-831
    • Xie, W.1    Barr, C.L.2    Kim, A.3
  • 7
    • 84946481204 scopus 로고    scopus 로고
    • WASP: allele-specific software for robust molecular quantitative trait locus discovery
    • van de Geijn B, McVicker G, Gilad Y, et al.: WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods. 2015; 12(11): 1061-1063.
    • (2015) Nat Methods , vol.12 , Issue.11 , pp. 1061-1063
    • van de Geijn, B.1    McVicker, G.2    Gilad, Y.3
  • 8
    • 80052851950 scopus 로고    scopus 로고
    • Mouse genomic variation and its effect on phenotypes and gene regulation
    • Keane TM, Goodstadt L, Danecek P, et al.: Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011; 477(7364): 289-294.
    • (2011) Nature , vol.477 , Issue.7364 , pp. 289-294
    • Keane, T.M.1    Goodstadt, L.2    Danecek, P.3
  • 9
    • 84941636443 scopus 로고    scopus 로고
    • Tools and best practices for data processing in allelic expression analysis
    • Castel SE, Levy-Moonshine A, Mohammadi P, et al.: Tools and best practices for data processing in allelic expression analysis. Genome Biol. 2015; 16: 195.
    • (2015) Genome Biol , vol.16 , pp. 195
    • Castel, S.E.1    Levy-Moonshine, A.2    Mohammadi, P.3
  • 10
    • 84952861819 scopus 로고    scopus 로고
    • HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
    • Servant N, Varoquaux N, Lajoie BR, et al.: HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015; 16: 259.
    • (2015) Genome Biol , vol.16 , pp. 259
    • Servant, N.1    Varoquaux, N.2    Lajoie, B.R.3
  • 11
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4): 357-359.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 12
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5): 589-595.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 13
    • 84926519013 scopus 로고    scopus 로고
    • HISAT: a fast spliced aligner with low memory requirements
    • Kim D, Langmead B, Salzberg SL: HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4): 357-360.
    • (2015) Nat Methods , vol.12 , Issue.4 , pp. 357-360
    • Kim, D.1    Langmead, B.2    Salzberg, S.L.3
  • 14
    • 84871809302 scopus 로고    scopus 로고
    • STAR: ultrafast universal RNA-seq aligner
    • Dobin A, Davis CA, Schlesinger F, et al.: STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29(1): 15-21.
    • (2013) Bioinformatics , vol.29 , Issue.1 , pp. 15-21
    • Dobin, A.1    Davis, C.A.2    Schlesinger, F.3
  • 15
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16): 2078-2079.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 16
    • 85010925319 scopus 로고    scopus 로고
    • QC Fail. 2016.
    • (2016) QC Fail
  • 17
    • 84938910089 scopus 로고    scopus 로고
    • Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression
    • Strogantsev R, Krueger F, Yamazawa K, et al.: Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression. Genome Biol. 2015; 16(1): 112.
    • (2015) Genome Biol , vol.16 , Issue.1 , pp. 112
    • Strogantsev, R.1    Krueger, F.2    Yamazawa, K.3
  • 18
    • 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, et al.: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4): R36.
    • (2013) Genome Biol , vol.14 , Issue.4 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3
  • 19
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, van Berkum NL, Williams L, et al.: Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950): 289-293.
    • (2009) Science , vol.326 , Issue.5950 , pp. 289-293
    • Lieberman-Aiden, E.1    van Berkum, N.L.2    Williams, L.3
  • 20
    • 84923366733 scopus 로고    scopus 로고
    • Chromatin architecture reorganization during stem cell differentiation
    • Dixon JR, Jung I, Selvaraj S, et al.: Chromatin architecture reorganization during stem cell differentiation. Nature. 2015; 518(7539): 331-336.
    • (2015) Nature , vol.518 , Issue.7539 , pp. 331-336
    • Dixon, J.R.1    Jung, I.2    Selvaraj, S.3
  • 21
    • 84919949716 scopus 로고    scopus 로고
    • A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
    • Rao SS, Huntley MH, Durand NC, et al.: A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7): 1665-1680.
    • (2014) Cell , vol.159 , Issue.7 , pp. 1665-1680
    • Rao, S.S.1    Huntley, M.H.2    Durand, N.C.3
  • 22
    • 84969685671 scopus 로고    scopus 로고
    • HiCUP: pipeline for mapping and processing Hi-C data [version 1; referees: 2 approved, 1 approved with reservations]
    • Wingett S, Ewels P, Furlan-Magaril M, et al.: HiCUP: pipeline for mapping and processing Hi-C data [version 1; referees: 2 approved, 1 approved with reservations]. F1000Res. 2015; 4: 1310.
    • (2015) F1000Res , vol.4 , pp. 1310
    • Wingett, S.1    Ewels, P.2    Furlan-Magaril, M.3
  • 23
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
    • Krueger F, Andrews SR: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011; 27(11): 1571-1572.
    • (2011) Bioinformatics , vol.27 , Issue.11 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.