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|Title:||Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads|
|Keywords:||Isoform level expression;RNA-seq data;MMSEQ|
|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.|
|Appears in Collections:||Dept of Mathematics Research Papers|
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