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Genome Biol. 2011;12(2):R13. doi: 10.1186/gb-2011-12-2-r13. Epub 2011 Feb 10.

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

Author information

1
Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK. ernest.turro@ic.ac.uk

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.

PMID:
21310039
PMCID:
PMC3188795
DOI:
10.1186/gb-2011-12-2-r13
[Indexed for MEDLINE]
Free PMC Article

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