694 related articles for article (PubMed ID: 21775302)
1. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
Grant GR; Farkas MH; Pizarro AD; Lahens NF; Schug J; Brunk BP; Stoeckert CJ; Hogenesch JB; Pierce EA
Bioinformatics; 2011 Sep; 27(18):2518-28. PubMed ID: 21775302
[TBL] [Abstract][Full Text] [Related]
2. TopHat: discovering splice junctions with RNA-Seq.
Trapnell C; Pachter L; Salzberg SL
Bioinformatics; 2009 May; 25(9):1105-11. PubMed ID: 19289445
[TBL] [Abstract][Full Text] [Related]
3. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
Zhang Y; Lameijer EW; 't Hoen PA; Ning Z; Slagboom PE; Ye K
Bioinformatics; 2012 Feb; 28(4):479-86. PubMed ID: 22219203
[TBL] [Abstract][Full Text] [Related]
4. JAGuaR: junction alignments to genome for RNA-seq reads.
Butterfield YS; Kreitzman M; Thiessen N; Corbett RD; Li Y; Pang J; Ma YP; Jones SJ; Birol İ
PLoS One; 2014; 9(7):e102398. PubMed ID: 25062255
[TBL] [Abstract][Full Text] [Related]
5. STAR: ultrafast universal RNA-seq aligner.
Dobin A; Davis CA; Schlesinger F; Drenkow J; Zaleski C; Jha S; Batut P; Chaisson M; Gingeras TR
Bioinformatics; 2013 Jan; 29(1):15-21. PubMed ID: 23104886
[TBL] [Abstract][Full Text] [Related]
6. Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG; Steijger T; Sipos B; Grant GR; Kahles A; Rätsch G; Goldman N; Hubbard TJ; Harrow J; Guigó R; Bertone P;
Nat Methods; 2013 Dec; 10(12):1185-91. PubMed ID: 24185836
[TBL] [Abstract][Full Text] [Related]
7. Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.
Hayer KE; Pizarro A; Lahens NF; Hogenesch JB; Grant GR
Bioinformatics; 2015 Dec; 31(24):3938-45. PubMed ID: 26338770
[TBL] [Abstract][Full Text] [Related]
8. Simulation-based comprehensive benchmarking of RNA-seq aligners.
Baruzzo G; Hayer KE; Kim EJ; Di Camillo B; FitzGerald GA; Grant GR
Nat Methods; 2017 Feb; 14(2):135-139. PubMed ID: 27941783
[TBL] [Abstract][Full Text] [Related]
9. Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.
Zhang Y; Liu X; MacLeod J; Liu J
BMC Genomics; 2018 Dec; 19(1):971. PubMed ID: 30591034
[TBL] [Abstract][Full Text] [Related]
10. Supersplat--spliced RNA-seq alignment.
Bryant DW; Shen R; Priest HD; Wong WK; Mockler TC
Bioinformatics; 2010 Jun; 26(12):1500-5. PubMed ID: 20410051
[TBL] [Abstract][Full Text] [Related]
11. A probabilistic framework for aligning paired-end RNA-seq data.
Hu Y; Wang K; He X; Chiang DY; Prins JF; Liu J
Bioinformatics; 2010 Aug; 26(16):1950-7. PubMed ID: 20576625
[TBL] [Abstract][Full Text] [Related]
12. OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
Wu J; Anczuków O; Krainer AR; Zhang MQ; Zhang C
Nucleic Acids Res; 2013 May; 41(10):5149-63. PubMed ID: 23571760
[TBL] [Abstract][Full Text] [Related]
13. Mapping RNA-seq Reads with STAR.
Dobin A; Gingeras TR
Curr Protoc Bioinformatics; 2015 Sep; 51():11.14.1-11.14.19. PubMed ID: 26334920
[TBL] [Abstract][Full Text] [Related]
14. CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data.
Kumar PK; Hoang TV; Robinson ML; Tsonis PA; Liang C
Sci Rep; 2015 Aug; 5():13443. PubMed ID: 26304587
[TBL] [Abstract][Full Text] [Related]
15. Optimizing RNA-Seq Mapping with STAR.
Dobin A; Gingeras TR
Methods Mol Biol; 2016; 1415():245-62. PubMed ID: 27115637
[TBL] [Abstract][Full Text] [Related]
16. Prediction and Quantification of Splice Events from RNA-Seq Data.
Goldstein LD; Cao Y; Pau G; Lawrence M; Wu TD; Seshagiri S; Gentleman R
PLoS One; 2016; 11(5):e0156132. PubMed ID: 27218464
[TBL] [Abstract][Full Text] [Related]
17. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ
BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805
[TBL] [Abstract][Full Text] [Related]
18. PASTA: splice junction identification from RNA-sequencing data.
Tang S; Riva A
BMC Bioinformatics; 2013 Apr; 14():116. PubMed ID: 23557086
[TBL] [Abstract][Full Text] [Related]
19. Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants.
Stein S; Bahrami-Samani E; Xing Y
Methods Mol Biol; 2017; 1648():129-142. PubMed ID: 28766294
[TBL] [Abstract][Full Text] [Related]
20. RNA-Seq read alignments with PALMapper.
Jean G; Kahles A; Sreedharan VT; De Bona F; Rätsch G
Curr Protoc Bioinformatics; 2010 Dec; Chapter 11():Unit 11.6. PubMed ID: 21154708
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]