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

• Main Authors: Alaimo, S. (Author), Bertoni, F. (Author), Bosotti, R. (Author), Cascione, L. (Author), Di Bella, S. (Author), Ferro, A. (Author), La Ferlita, A. (Author), Laliotis, G.I (Author), Martorana, E. (Author), Pulvirenti, A. (Author), Tsichlis, P.N (Author)
• Format: Article
• Language: English
• Published: BioMed Central Ltd 2021
• Subjects: Biological species; biology; cloud computing; Cloud Computing; Cloud deployment; Cloud environments; Commercial software; Computational approach; Computational Biology; data analysis; Data Analysis; Data handling; Differential expression analysis; Docker; Graphical user interfaces; high throughput sequencing; High-Throughput Nucleotide Sequencing; Information analysis; ncRNAs; Non-coding RNAs; Pathway analysis; Pipeline; Polymerase chain reaction; Research laboratories; RNA; RNA-seq; RNA-Seq; Rna-seq data analysis; sequence analysis; Sequence Analysis, RNA; software; Software; Stand-alone software; Technical background; Transcriptome profiling
• Online Access: View Fulltext in Publisher

 Background: 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. Results: 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. Conclusions: 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. © 2021, The Author(s).