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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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BYASE: a Python library for estimating gene and isoform level allele-specific expression.

Lili Dong1, Jianan Wang1, Guohua Wang1,2

  • 1School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.

Bioinformatics (Oxford, England)
|July 18, 2020
PubMed
Summary
This summary is machine-generated.

We developed BYASE, a Python package, and BYASE-GUI, a graphical tool, to identify allele-specific expression (ASE) using Bayesian inference from RNA-seq data. These tools support gene and isoform levels, phased and non-phased SNPs, and polyploid organisms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Allele-specific expression (ASE) plays a crucial role in various biological processes.
  • Accurate identification of ASE is essential for understanding gene regulation and function.

Purpose of the Study:

  • To introduce BYASE, a novel Python package, and BYASE-GUI, a graphical user interface (GUI) tool.
  • To provide a robust method for identifying allele-specific expression from RNA-seq data.

Main Methods:

  • Utilizes Bayesian inference for ASE identification.
  • Supports both single-end and paired-end RNA-seq data.
  • Accommodates phased and non-phased SNPs and is applicable to polyploid organisms.

Main Results:

  • BYASE and BYASE-GUI enable simultaneous reporting of gene-level and isoform-level expression differences.
  • The tools offer a flexible approach to ASE analysis.

Conclusions:

  • BYASE and BYASE-GUI provide valuable computational tools for researchers studying allele-specific expression.
  • The open-source availability facilitates broader adoption and further development in the field.