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. © 2011 Turro et al.; licensee BioMed Central Ltd.
CITATION STYLE
Turro, E., Su, S. Y., Gonçalves, Â., Coin, L. J. M., Richardson, S., & Lewin, A. (2011). Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biology, 12(2). https://doi.org/10.1186/gb-2011-12-2-r13
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