Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
ErnestTurro;
Shu-YiSu;
ÂngelaGonçalves;
Lachlan JMCoin;
SylviaRichardson;
Alex Lewin 
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(2011)
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Genome Biol, 12 (2).
R13-.
ISSN 1474-760X
DOI: 10.1186/gb-2011-12-2-r13
;
(2011)
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Genome Biol, 12 (2).
R13-.
ISSN 1474-760X
DOI: 10.1186/gb-2011-12-2-r13
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.
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picture_as_pdf - Haplotype and isoform_GOLD VoR.pdf
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- Available under Creative Commons: 3.0
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- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188795 (OA Location)
- 10.1186/gb-2011-12-2-r13 (DOI)
- 21310039 (PubMed)