Journal
COMPUTERS IN BIOLOGY AND MEDICINE
Volume 110, Issue -, Pages 234-243Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.compbiomed.2019.05.019
Keywords
microRNA; Gene expression profiling; Color-space; Base-space; Bioinformatics pipeline
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Funding
- Institutional Research Funds (Italian Ministry of Health)
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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data, but usually they are limited by many factors including: inaccurate processing, lack of optimal parameterization, outdated references plus annotations, restrictions in uploading large datasets, and shortage of biological inferences.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.
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