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

被引：0

作者：

Ernest Turro

Shu-Yi Su

Ângela Gonçalves

Lachlan JM Coin

Sylvia Richardson

Alex Lewin

机构：

[1] Imperial College London,Department of Epidemiology and Biostatistics

[2] University of California,Ernest Gallo Clinic and Research Center, Department of Bioinformatics

[3] San Francisco,undefined

[4] European Bioinformatics Institute (EMBL-EBI),undefined

来源：

Genome Biology | / 12卷

关键词：

Expectation Maximization; Allelic Imbalance; Expression Estimate; Cassette Exon; Diploid Organism;

D O I：

暂无

中图分类号：

学科分类号：

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.

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