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

Ernest Turro1*, Shu-Yi Su2, Ângela Gonçalves3, Lachlan JM Coin1, Sylvia Richardson1 and Alex Lewin1

Author Affiliations

1 Department of Epidemiology and Biostatistics, Imperial College London, Norfolk Place, London, W2 1PG, UK

2 Ernest Gallo Clinic and Research Center, Department of Bioinformatics, University of California, San Francisco, 5858 Horton Street, Suite 200, Emeryville, CA 94608, USA

3 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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Genome Biology 2011, 12:R13  doi:10.1186/gb-2011-12-2-r13

Published: 10 February 2011


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.