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

Turro, Ernest, Su, Shu-Yi, Goncalves, Ângela, Coin, Lachlan J. M., Richardson, Sylvia and Lewin, Alex (2011) Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biology, 12 2: R13.1-R13.15. doi:10.1186/gb-2011-12-2-r13


Author Turro, Ernest
Su, Shu-Yi
Goncalves, Ângela
Coin, Lachlan J. M.
Richardson, Sylvia
Lewin, Alex
Title Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-7596
1474-760X
Publication date 2011-02-10
Sub-type Article (original research)
DOI 10.1186/gb-2011-12-2-r13
Open Access Status DOI
Volume 12
Issue 2
Start page R13.1
End page R13.15
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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