Intron-centric estimation of alternative splicing from RNA-seq data

Bioinformatics

Volumn 29, Issue 2, 2013, Pages 273-274

  Pervouchine, Dmitri D ^a,b,c   Knowles, David G ^a,b   Guigó, Roderic ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ARTICLE; COMPUTER PROGRAM; EXON; HIGH THROUGHPUT SEQUENCING; HUMAN; INTRON; RNA SPLICING; SEQUENCE ANALYSIS;

ALTERNATIVE SPLICING; EXONS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTRONS; RNA SPLICE SITES; SEQUENCE ANALYSIS, RNA; SOFTWARE;

MLCS; MLOWN;

EID: 84872541952     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts678     Document Type: Article

References (7)

1. Kakaradov, B. et al. (2012) Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. BMC Bioinformatics, 13 (Suppl. 6), S11.
2. Katz, Y. et al. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
3. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
4. Montgomery, S. et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 464, 773-777.
5. Pan, Q. et al. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
6. Tilgner, H. et al. (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res., 22, 1616-1625.
7. Trapnell, C. et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc., 7, 562-578.