Large-scale RNAseq has substantially changed the transcriptomics field, as it enables an unprecedented amount of high resolution data to be acquired. However, the analysis of these data still poses a challenge to the research community. Many tools have been developed to overcome this problem, and to facilitate the study of miRNA expression profiles and those of their target genes. While a few of these enable both kinds of analysis to be performed, they also present certain limitations in terms of their requirements and/or the restrictions on data uploading.
To avoid these restraints, researchers from the CSIC/University of Seville have developed a suite that offers the identification of miRNA, mRNA and circRNAs that can be applied to any sequenced organism. Additionally, it enables differential expression, miRNA-mRNA target prediction and/or functional analysis. The miARma-Seq pipeline is presented as a stand-alone tool that is both easy to install and flexible in terms of its use, and that brings together well-established software in a single bundle. This suite can analyze a large number of samples due to its multithread design. By testing miARma-Seq in validated datasets, the researchers demonstrate here the benefits that can be gained from this tool by making it readily accessible to the research community.
miARma-Seq pipeline workflow
An overview of the modular design of the pipeline. Main modules are indicated by gray background. Output files are indicated by purple background.
Availability – The miARma-Seq tools are avialable at: http://miarmaseq.cbbio.es/