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

Alessandro La Ferlita,Francesco Bertoni,Georgios I Laliotis,Salvatore Alaimo,Alfredo Pulvirenti,Emanuele Martorana,Alfredo Ferro,Sebastiano Di Bella,Luciano Cascione,Philip N Tsichlis,Roberta Bosotti

doi:10.1186/s12859-021-04211-7

Abstract

BackgroundRNA-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.ResultsMotivated 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.ConclusionsRNAdetector 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.

Highlights

RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules
Software introduction RNAdetector was designed as an easy-to-use, flexible, cross-platform, and comprehensive pipeline, allowing users to analyze mRNAs and non-coding RNAs (ncRNAs)
Several classes of Human, Mouse, and C.elegans ncRNAs such as miRNAs, piwi-associated RNAs (piRNAs) [only for human at this moment], small nucleolar RNAs (snoRNAs), long non-coding RNAs (lncRNAs), transcribed ultraconserved regions (t-UCRs) [only for human at this moment], circRNAs, and tRNA-derived ncRNAs classes reported in tRFexplorer [61] and tRFdb [62] are already stored in the remote repository of RNAdetector

Summary

Introduction

RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules 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. RNA-Seq can be used to detect non-coding RNAs (ncRNAs), namely, RNA molecules that do not encode for proteins but represent a considerable amount of the transcriptome involved in many aspects of cell physiology [2, 3] They act by regulating a broad spectrum of cellular processes, controlling gene expression, and contributing to genome organization and stability [3]. RNA-Seq produces a dramatically higher amount of data than other traditional technologies, such as Real-Time PCR or microarray, demanding fast and effective computational approaches [4]

Results

Discussion

Conclusion