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Title: Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
Authors: Turro, E
Su, SY
Gonçalves, A
Coin, LJM
Richardson, S
Lewin, A
Keywords: Isoform level expression;RNA-seq data;MMSEQ
Issue Date: 2011
Publisher: BioMed Central
Citation: Genome Biology, 12:R13, (2011)
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.
ISSN: 1474-7596
Appears in Collections:Dept of Mathematics Research Papers

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