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RNA-Seq-Based Transcript Structure Analysis with TrBorderExt.

Yejun Wang1, Ming-An Sun2, Aaron P White3

  • 1Department of Cell Biology and Genetics, School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, P.R. China. wangyj@szu.edu.cn.

Methods in Molecular Biology (Clifton, N.J.)
|March 7, 2018
PubMed
Summary
This summary is machine-generated.

Directional RNA-Sequencing (RNA-Seq) offers cost-effective gene expression analysis in bacteria. A new tool, TrBorderExt, accurately identifies bacterial transcript start and termination sites from RNA-Seq data.

Keywords:
Directional RNA-SeqOperonTranscript borderTranscript start siteTranscript termination siteTranscript unit

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • RNA-Sequencing (RNA-Seq) is a standard method for bacterial gene expression studies.
  • Directional RNA-Seq provides medium-resolution transcript border analysis at a lower cost compared to other methods.
  • Accurate identification of transcript start and termination sites is crucial for understanding bacterial gene regulation.

Purpose of the Study:

  • To develop a computational tool for precise identification of bacterial transcript start sites (TSS) and termination sites (TTS).
  • To facilitate the analysis of transcript structures from directional RNA-Seq datasets.
  • To provide a user-friendly protocol for applying the developed software to raw RNA-Seq data.

Main Methods:

  • Development of the TrBorderExt software package using Perl and R programming languages.
  • Implementation of algorithms to parse transcript start and termination sites from RNA-Seq data.
  • Detailed protocol creation for step-by-step usage of the software.

Main Results:

  • TrBorderExt accurately identifies bacterial transcript start and termination sites.
  • The software enables detailed transcript structure analysis from directional RNA-Seq data.
  • A comprehensive protocol is provided for using TrBorderExt on raw RNA-Seq data.

Conclusions:

  • TrBorderExt is an effective tool for analyzing bacterial transcript borders using directional RNA-Seq.
  • The software enhances the utility of directional RNA-Seq for transcriptomic studies in bacteria.
  • TrBorderExt is freely accessible, promoting wider adoption in bacterial genomics research.