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- Title
Allelic imbalance metre ( Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
- Authors
Pandey, Ram Vinay; Franssen, Susanne U.; Futschik, Andreas; Schlötterer, Christian
- Abstract
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.
- Subjects
GENE expression; NUCLEOTIDE sequence; GENETIC polymorphisms; DROSOPHILA pseudoobscura; COMPUTER simulation
- Publication
Molecular Ecology Resources, 2013, Vol 13, Issue 4, p740
- ISSN
1755-098X
- Publication type
Article
- DOI
10.1111/1755-0998.12110