Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 109

1.

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.

Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36.

2.

GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment.

Zhang Z, Huang S, Wang J, Zhang X, Pardo Manuel de Villena F, McMillan L, Wang W.

Bioinformatics. 2013 Jul 1;29(13):i291-9. doi: 10.1093/bioinformatics/btt216.

3.

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. doi: 10.1002/0471250953.bi1106s32.

PMID:
21154708
4.

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 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

5.

RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.

Wilson GW, Stein LD.

Nucleic Acids Res. 2015 Oct 15;43(18):e122. doi: 10.1093/nar/gkv594. Epub 2015 Jun 16.

6.

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL.

Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16.

7.

HSA: a heuristic splice alignment tool.

Bu J, Chi X, Jin Z.

BMC Syst Biol. 2013;7 Suppl 2:S10. doi: 10.1186/1752-0509-7-S2-S10. Epub 2013 Dec 17.

8.

Mapping RNA-seq Reads with STAR.

Dobin A, Gingeras TR.

Curr Protoc Bioinformatics. 2015 Sep 3;51:11.14.1-19. doi: 10.1002/0471250953.bi1114s51. Review.

9.

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 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014.

10.

Supersplat--spliced RNA-seq alignment.

Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC.

Bioinformatics. 2010 Jun 15;26(12):1500-5. doi: 10.1093/bioinformatics/btq206. Epub 2010 Apr 21.

11.

OSA: a fast and accurate alignment tool for RNA-Seq.

Hu J, Ge H, Newman M, Liu K.

Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.

PMID:
22592379
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 1;41(10):5149-63. doi: 10.1093/nar/gkt216. Epub 2013 Apr 9.

13.

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 25;5:13443. doi: 10.1038/srep13443.

14.

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:S10. doi: 10.1186/1471-2105-16-S17-S10. Epub 2015 Dec 7.

15.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Liu C, Ma J, Chang CJ, Zhou X.

BMC Bioinformatics. 2013 Jun 15;14:193. doi: 10.1186/1471-2105-14-193.

16.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

Martínez H, Tárraga J, Medina I, Barrachina S, Castillo M, Dopazo J, Quintana-Ortí ES.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):995-1007. doi: 10.1109/TCBB.2015.2392077.

PMID:
26451814
17.

RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations.

Munger SC, Raghupathy N, Choi K, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH, Chesler EJ, Churchill GA.

Genetics. 2014 Sep;198(1):59-73. doi: 10.1534/genetics.114.165886.

18.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.

Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S, Wu TD.

BMC Med Genomics. 2011 Jan 24;4:11. doi: 10.1186/1755-8794-4-11.

19.

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. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11.

20.

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Kim D, Salzberg SL.

Genome Biol. 2011 Aug 11;12(8):R72. doi: 10.1186/gb-2011-12-8-r72.

Supplemental Content

Support Center