Manatee: detection and quantification of small ncRNAs from next-generation sequencing data
| Autor: | Artemis G. Hatzigeorgiou, Ioannis S. Vlachos, Spyros Tastsoglou, Joanna E. Handzlik |
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| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Gene isoform
Small RNA Computer science lcsh:Medicine Locus (genetics) Computational biology Short length Article DNA sequencing Transcriptome Annotation 03 medical and health sciences 0302 clinical medicine Computational platforms and environments Neoplasms biology.animal microRNA Manatee Humans Functional studies lcsh:Science 030304 developmental biology Abundance estimation 0303 health sciences Multidisciplinary biology Sequence Analysis RNA Gene Expression Profiling lcsh:R Computational Biology High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Hep G2 Cells Data processing Simulated data 030220 oncology & carcinogenesis Transfer RNA MCF-7 Cells RNA Small Untranslated lcsh:Q Software Algorithms Coding (social sciences) |
| Zdroj: | Scientific Reports DOAJ-Articles UnpayWall Microsoft Academic Graph PubMed Central bioRxiv Datacite ORCID Scientific Reports, Vol 10, Iss 1, Pp 1-10 (2020) |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-020-57495-9 |
| Popis: | Small non-coding RNAs (sncRNAs) play important roles in health and disease. Next Generation Sequencing (NGS) technologies are considered as the most powerful and versatile methodologies to explore small RNA (sRNA) transcriptomes in diverse experimental and clinical studies. Small RNA-Seq (sRNA-Seq) data analysis proved to be challenging due to non-unique genomic origin, short length, and abundant post-transcriptional modifications of sRNA species. Here, we present Manatee, an algorithm for the quantification of sRNA classes and the detection of novel expressed non-coding loci. Manatee combines prior annotation of sRNAs with reliable alignment density information and extensive rescue of usually neglected multimapped reads to provide accurate transcriptome-wide sRNA expression quantification. Comparison of Manatee against state-of-the-art implementations using real and simulated data demonstrates its high accuracy across diverse sRNA classes. Manatee also goes beyond common pipelines by identifying and quantifying expression from unannotated loci and microRNA isoforms (isomiRs). It is user-friendly, can be easily incorporated in pipelines, and provides a simplified output suitable for direct usage in downstream analyses and functional studies. |
| Databáze: | OpenAIRE |
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