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Oxford University Press (OUP), Bioinformatics, 24(25), p. 3207-3212

DOI: 10.1093/bioinformatics/btp579

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Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Journal article published in 2009 by Jacob F. Degner, John C. Marioni ORCID, Athma A. Pai, Joseph K. Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K. Pritchard
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).