Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
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ABSTRACT:
SUBMITTER: Turro E
PROVIDER: S-EPMC3188795 | biostudies-literature | 2011
REPOSITORIES: biostudies-literature
Publications
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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