124 related articles for article (PubMed ID: 22257667)
1. FX: an RNA-Seq analysis tool on the cloud.
Hong D; Rhie A; Park SS; Lee J; Ju YS; Kim S; Yu SB; Bleazard T; Park HS; Rhee H; Chong H; Yang KS; Lee YS; Kim IH; Lee JS; Kim JI; Seo JS
Bioinformatics; 2012 Mar; 28(5):721-3. PubMed ID: 22257667
[TBL] [Abstract][Full Text] [Related]
2. A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification.
Zhao S; Zhang B
BMC Genomics; 2015 Feb; 16(1):97. PubMed ID: 25765860
[TBL] [Abstract][Full Text] [Related]
3. SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.
Chu C; Li X; Wu Y
BMC Bioinformatics; 2015; 16 Suppl 17(Suppl 17):S10. PubMed ID: 26678515
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.
Stein S; Lu ZX; Bahrami-Samani E; Park JW; Xing Y
Nucleic Acids Res; 2015 Dec; 43(22):10612-22. PubMed ID: 26578562
[TBL] [Abstract][Full Text] [Related]
6. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.
D'Antonio M; D'Onorio De Meo P; Pallocca M; Picardi E; D'Erchia AM; Calogero RA; Castrignanò T; Pesole G
BMC Genomics; 2015; 16(Suppl 6):S3. PubMed ID: 26046471
[TBL] [Abstract][Full Text] [Related]
7. CAFU: a Galaxy framework for exploring unmapped RNA-Seq data.
Chen S; Ren C; Zhai J; Yu J; Zhao X; Li Z; Zhang T; Ma W; Han Z; Ma C
Brief Bioinform; 2020 Mar; 21(2):676-686. PubMed ID: 30815667
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. NGScloud: RNA-seq analysis of non-model species using cloud computing.
Mora-Márquez F; Vázquez-Poletti JL; López de Heredia U
Bioinformatics; 2018 Oct; 34(19):3405-3407. PubMed ID: 29726914
[TBL] [Abstract][Full Text] [Related]
10. wapRNA: a web-based application for the processing of RNA sequences.
Zhao W; Liu W; Tian D; Tang B; Wang Y; Yu C; Li R; Ling Y; Wu J; Song S; Hu S
Bioinformatics; 2011 Nov; 27(21):3076-7. PubMed ID: 21896507
[TBL] [Abstract][Full Text] [Related]
11. Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads.
Zhao S
PLoS One; 2014; 9(7):e101374. PubMed ID: 24992027
[TBL] [Abstract][Full Text] [Related]
12. Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.
Sand O; Thomas-Chollier M; van Helden J
Bioinformatics; 2009 Oct; 25(20):2739-40. PubMed ID: 19720677
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. 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]
15. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
Sultan M; Schulz MH; Richard H; Magen A; Klingenhoff A; Scherf M; Seifert M; Borodina T; Soldatov A; Parkhomchuk D; Schmidt D; O'Keeffe S; Haas S; Vingron M; Lehrach H; Yaspo ML
Science; 2008 Aug; 321(5891):956-60. PubMed ID: 18599741
[TBL] [Abstract][Full Text] [Related]
16. ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences.
Kim N; Shin S; Lee S
Nucleic Acids Res; 2004 Jul; 32(Web Server issue):W181-6. PubMed ID: 15215376
[TBL] [Abstract][Full Text] [Related]
17. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Pertea M; Kim D; Pertea GM; Leek JT; Salzberg SL
Nat Protoc; 2016 Sep; 11(9):1650-67. PubMed ID: 27560171
[TBL] [Abstract][Full Text] [Related]
18. 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]
19. A high-quality annotated transcriptome of swine peripheral blood.
Liu H; Smith TPL; Nonneman DJ; Dekkers JCM; Tuggle CK
BMC Genomics; 2017 Jun; 18(1):479. PubMed ID: 28646867
[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]
