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

Ernest Turro, Shu Yi Su, Ângela Gonçalves, Lachlan J.M. Coin, Sylvia Richardson, Alex Lewin

Research output: Contribution to journalArticlepeer-review

173 Scopus citations

Abstract

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.

Original languageEnglish
Article numberR13
JournalGenome Biology
Volume12
Issue number2
DOIs
StatePublished - 10 Feb 2011
Externally publishedYes

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