title: eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
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.
authors.forename: Tiezheng
authors.initials: T
authors.lastname: Yuan
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Huang
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Dittmar
authors.forename: Meijun
authors.initials: M
authors.lastname: Du
authors.forename: Manish
authors.initials: M
authors.lastname: Kohli
authors.forename: Lisa
authors.initials: L
authors.lastname: Boardman
authors.forename: Stephen N
authors.initials: SN
authors.lastname: Thibodeau
authors.affiliation: Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee WI 53226, USA. liwang@mcw.edu.
authors.forename: Liang
authors.initials: L
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger