Introduction

RNA-sequencing (RNA-seq) has become an established way for measuring gene expression in model organisms and humans. While methods development for refining the corresponding data processing and analysis pipeline is ongoing, protocols for typical steps have been proposed and are widely used. Several user interfaces have been developed for making such analysis steps accessible to life scientists without extensive knowledge of command line tools. We performed a systematic search and evaluation of such interfaces to investigate to what extent these can indeed facilitate RNA-seq data analysis. We found a total of 29 open source interfaces, and six of the more widely used interfaces were evaluated in detail. Central criteria for evaluation were ease of configuration, documentation, usability, computational demand and reporting. No interface scored best in all of these criteria, indicating that the final choice will depend on the specific perspective of users and the corresponding weighting of criteria. Considerable technical hurdles had to be overcome in our evaluation. For many users, this will diminish potential benefits compared with command line tools, leaving room for future improvement of interfaces.

Publications

  1. Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.
    Cite this
    Poplawski A, Marini F, Hess M, Zeller T, Mazur J, Binder H, 2016-03-01 - Briefings in bioinformatics

Credits

  1. Alicia Poplawski
    Developer

  2. Federico Marini
    Developer

  3. Moritz Hess
    Developer

  4. Tanja Zeller
    Developer

  5. Johanna Mazur
    Developer

  6. Harald Binder
    Investigator

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Summary
AccessionBT000148
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByHarald Binder