Background: One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability\nto examine the allelic imbalance of the expression of a gene. This process is often a complex task that entails quality\ncontrol, alignment, and the counting of reads over heterozygous single-nucleotide polymorphisms. Allelic imbalance\nanalysis is subject to technical biases, due to differences in the sequences of the measured alleles. Flexible bioinformatics\ntools are needed to ease the workflow while retaining as much RNA sequencing information as possible throughout the\nanalysis to detect and address the possible biases.\nResults: We present AllelicImblance, a software program that is designed to detect, manage, and visualize allelic\nimbalances comprehensively. The purpose of this software is to allow users to pose genetic questions in any RNA\nsequencing experiment quickly, enhancing the general utility of RNA sequencing. The visualization features can reveal\nnotable, non-trivial allelic imbalance behavior over specific regions, such as exons.\nConclusions: The software provides a complete framework to perform allelic imbalance analyses of aligned RNA\nsequencing data, from detection to visualization, within the robust and versatile management class, ASEset.
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