CBS-miRSeq: A comprehensive tool for accurate and extensive analyses of microRNA-sequencing data

Computers in Biology and Medicine

20 June Jun 2019 3 months ago
  • Chiesa M, Colombo GI

Several online and local tools have been developed to analyze microRNA-sequencing (miRNA-Seq) data, but usually they are limited by many factors including: inaccurate processing, lack of optimal parameterization, outdated references plus annotations, restrictions in uploading large datasets, and shortage of biological inferences. In this work, we have developed a fully customized bioinformatics analysis pipeline (Color and Base-Space miRNA-Seq - CBS-miRSeq) for the seamless processing of short-reads miRNA-Seq data. The pipeline has been designed using Bash, Perl, and R scripts. CBS-miRSeq includes modules for read pre- and post-processing (quality assessment, filtering, adapter trimming and mapping) and different types of downstream analyses (identification of miRNA variants (isomiRs), novel miRNA prediction, miRNA:mRNA interaction target prediction, robust differential miRNA analysis, and target gene functional analysis). In this manuscript, we show that re-analysis of two published datasets using the CBS-miRSeq pipeline leads to better performance and efficiency in terms of their pipelines set and biomarker discovery between two biological conditions.

Reference

Kesharwani RK, Chiesa M, Bellazzi R, Colombo GI. CBS-miRSeq: A comprehensive tool for accurate and extensive analyses of microRNA-sequencing data. Comput Biol Med 2019 Jun 1;110:234-243. doi: 10.1016/j.compbiomed.2019.05.019

Go to PubMed