title: Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
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.
authors.affiliation: Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.
authors.forename: Ram Vinay
authors.initials: RV
authors.lastname: Pandey
authors.forename: Susanne U
authors.initials: SU
authors.lastname: Franssen
authors.forename: Andreas
authors.initials: A
authors.lastname: Futschik
authors.forename: Christian
authors.initials: C
authors.lastname: Schlötterer
mesh_terms: D022981:Allelic Imbalance; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*