Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

被引：179

作者：

Turro, Ernest ^{[1
]}

Su, Shu-Yi ^{[2
]}

Goncalves, Angela ^{[3
]}

Coin, Lachlan J. M. ^{[1
]}

Richardson, Sylvia ^{[1
]}

Lewin, Alex ^{[1
]}

机构：

[1] Univ London Imperial Coll Sci Technol & Med, Dept Epidemiol & Biostat, London W2 1PG, England

[2] Univ Calif San Francisco, Ernest Gallo Clin & Res Ctr, Dept Bioinformat, Emeryville, CA 94608 USA

[3] European Bioinformat Inst EMBL EBI, Cambridge CB10 1SD, England

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 02期

基金：

英国生物技术与生命科学研究理事会;

关键词：

ORIGIN ALLELIC EXPRESSION;

D O I：

10.1186/gb-2011-12-2-r13

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown, the two parental isoform sequences can be individually reconstructed. A new statistical method, MMSEQ, deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). Our software can take into account non-uniform read generation and works with paired-end reads.

引用

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