ERNA: A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing

Tiezheng Yuan, Xiaoyi Huang, Rachel L. Dittmar, Meijun Du, Manish Kohli, Lisa Allyn Boardman, Stephen N Thibodeau, Liang Wang

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background: RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by high throughput sequencers.Results: We developed a standalone tool with graphic user interface (GUI)-based analytic modules, known as eRNA. The capacity of performing parallel processing and sample management facilitates large data analyses by maximizing hardware usage and freeing users from tediously handling sequencing data. The module miRNA identification" includes GUIs for raw data reading, adapter removal, sequence alignment, and read counting. The module " mRNA identification" includes GUIs for reference sequences, genome mapping, transcript assembling, and differential expression. The module " Target screening" provides expression profiling analyses and graphic visualization. The module " Self-testing" offers the directory setups, sample management, and a check for third-party package dependency. Integration of other GUIs including Bowtie, miRDeep2, and miRspring extend the program's functionality.Conclusions: eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. eRNA is available for free download at https://sourceforge.net/projects/erna/?source=directory.

Original languageEnglish (US)
Article number176
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Mar 5 2014

Fingerprint

High-Throughput Nucleotide Sequencing
Directories
MicroRNAs
RNA Sequence Analysis
Messenger RNA
Sequence Alignment
Chromosome Mapping
Computational Biology
Research
Reading
Software

Keywords

  • Bioinformatics tool
  • Graphic user interface
  • Parallel processing
  • RNA sequencing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

ERNA : A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. / Yuan, Tiezheng; Huang, Xiaoyi; Dittmar, Rachel L.; Du, Meijun; Kohli, Manish; Boardman, Lisa Allyn; Thibodeau, Stephen N; Wang, Liang.

In: BMC Genomics, Vol. 15, No. 1, 176, 05.03.2014.

Research output: Contribution to journalArticle

Yuan, Tiezheng ; Huang, Xiaoyi ; Dittmar, Rachel L. ; Du, Meijun ; Kohli, Manish ; Boardman, Lisa Allyn ; Thibodeau, Stephen N ; Wang, Liang. / ERNA : A graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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