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

BMC Bioinformatics

Georgios I. Laliotis¹  Philip N. Tsichlis¹  Salvatore Alaimo²  Alfredo Pulvirenti²  Alfredo Ferro²  Alessandro La Ferlita³  Francesco Bertoni⁴  Luciano Cascione⁴  Sebastiano Di Bella⁵  Roberta Bosotti⁵  Emanuele Martorana⁶ 

[1] Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA;Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy;Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy;Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA;Department of Physics and Astronomy, University of Catania, Catania, Italy;Institute of Oncology Research, Bellinzona, Switzerland;Nerviano Medical Sciences, Nerviano, Milan, Italy;Regional Referral Centre for Rare Lung Diseases, A. O. U. “Policlinico-Vittorio Emanuele”, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy;

关键词: RNA-seq;    Stand-alone software;    Cloud deployment;    Pipeline;    Docker;    ncRNAs;    Differential expression analysis;    Pathway analysis;   

DOI  :  10.1186/s12859-021-04211-7

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY