RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis

• Published in: BMC bioinformatics Vol. 22; no. 1; pp. 1 - 298
• Main Authors: La Ferlita, Alessandro, Alaimo, Salvatore, Di Bella, Sebastiano, Martorana, Emanuele, Laliotis, Georgios I, Bertoni, Francesco, Cascione, Luciano, Tsichlis, Philip N, Ferro, Alfredo, Bosotti, Roberta, Pulvirenti, Alfredo
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 03.06.2021; BioMed Central; BMC
• Subjects: Applications software; Bioinformatics; Cloud computing; Cloud deployment; Computational biology; Computer applications; Computer graphics; Computer programs; Data analysis; Docker; Gene expression; Genomes; Graphical user interface; Laboratories; Methods; ncRNAs; Non-coding RNA; Operating systems; Outsourcing; Pipeline; RNA sequencing; RNA-seq; Servers; Software; Stand-alone software; Technology; Transcriptomes; User interface; Italy
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-021-04211-7

RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requiring sophisticated computational approaches for their analysis than other traditional technologies such as Real-Time PCR or microarrays, strongly discouraging non-expert users. For this reason, dozens of pipelines have been deployed for the analysis of RNA-Seq data. Although interesting, these present several limitations and their usage require a technical background, which may be uncommon in small research laboratories. Therefore, the application of these technologies in such contexts is still limited and causes a clear bottleneck in knowledge advancement. Motivated by these considerations, we have developed RNAdetector, a new free cross-platform and user-friendly RNA-Seq data analysis software that can be used locally or in cloud environments through an easy-to-use Graphical User Interface allowing the analysis of coding and non-coding RNAs from RNA-Seq datasets of any sequenced biological species. RNAdetector is a new software that fills an essential gap between the needs of biomedical and research labs to process RNA-Seq data and their common lack of technical background in performing such analysis, which usually relies on outsourcing such steps to third party bioinformatics facilities or using expensive commercial software.