Please use this identifier to cite or link to this item:
http://bura.brunel.ac.uk/handle/2438/11568
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. |
URI: | http://www.genomebiology.com/2011/12/2/R13 http://bura.brunel.ac.uk/handle/2438/11568 |
DOI: | http://dx.doi.org/10.1186/gb-2011-12-2-r13 |
ISSN: | 1474-7596 1474-760X |
Appears in Collections: | Dept of Mathematics Research Papers |
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Fulltext.pdf | 3.09 MB | Adobe PDF | View/Open |
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