Journal
MOLECULAR ECOLOGY RESOURCES
Volume 13, Issue 4, Pages 740-745Publisher
WILEY
DOI: 10.1111/1755-0998.12110
Keywords
allele-specific gene expression; allelic imbalance; gene expression; mapping bias; RNA-seq
Funding
- Austrian Science Funds (FWF) [P22834]
- Volkswagen Foundation
- Austrian Science Fund (FWF) [P 22834] Funding Source: researchfish
- Austrian Science Fund (FWF) [P22834] Funding Source: Austrian Science Fund (FWF)
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Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user-friendly software tool, Allim, to estimate allele-specific gene expression. Because mapping bias is a major problem for reliable estimates of allele-specific gene expression using RNA-seq, Allim combines two different strategies to account for the mapping biases. In order to reduce the mapping bias, Allim first generates a polymorphism-aware reference genome that accounts for the sequence variation between the alleles. Then, a sequence-specific simulation tool estimates the residual mapping bias. Statistical tests for allelic imbalance are provided that can be used with the bias corrected RNA-seq data.
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