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


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.

SUBMITTER: Turro E 

PROVIDER: S-EPMC3188795 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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

Turro Ernest E   Su Shu-Yi SY   Gonçalves Ângela    Coin Lachlan J M LJ   Richardson Sylvia S   Lewin Alex A  

Genome biology 20110210 2


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 ge  ...[more]

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