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Article

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.

Bioinformatics (Oxford, England) - 1 Jul 2018

Raghupathy Narayanan, Choi Kwangbom, Vincent Matthew J, Beane Glen L, Sheppard Keith S, Munger Steven C, Korstanje Ron, Pardo-Manual de Villena Fernando, Churchill Gary A

Abstract excerpt

Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, read-mapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to...

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PMID: 29444201
DOI: 10.1093/bioinformatics/bty078
PMCID: PMC6022640

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