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DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing ev...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823405/ https://www.ncbi.nlm.nih.gov/pubmed/33396959 http://dx.doi.org/10.3390/genes12010046 |
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author | Alexiou, Athanasios Zisis, Dimitrios Kavakiotis, Ioannis Miliotis, Marios Koussounadis, Antonis Karagkouni, Dimitra Hatzigeorgiou, Artemis G. |
author_facet | Alexiou, Athanasios Zisis, Dimitrios Kavakiotis, Ioannis Miliotis, Marios Koussounadis, Antonis Karagkouni, Dimitra Hatzigeorgiou, Artemis G. |
author_sort | Alexiou, Athanasios |
collection | PubMed |
description | microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing every research aspect in the fields of biology and medicine. Particularly, small RNA-Seq (sRNA-Seq) enables small non-coding RNA quantification on a high-throughput scale, providing a closer look into the expression profiles of these crucial regulators within the cell. Here, we present DIANA-microRNA-Analysis-Pipeline (DIANA-mAP), a fully automated computational pipeline that allows the user to perform miRNA NGS data analysis from raw sRNA-Seq libraries to quantification and Differential Expression Analysis in an easy, scalable, efficient, and intuitive way. Emphasis has been given to data pre-processing, an early, critical step in the analysis for the robustness of the final results and conclusions. Through modularity, parallelizability and customization, DIANA-mAP produces high quality expression results, reports and graphs for downstream data mining and statistical analysis. In an extended evaluation, the tool outperforms similar tools providing pre-processing without any adapter knowledge. Closing, DIANA-mAP is a freely available tool. It is available dockerized with no dependency installations or standalone, accompanied by an installation manual through Github. |
format | Online Article Text |
id | pubmed-7823405 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-78234052021-01-24 DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification Alexiou, Athanasios Zisis, Dimitrios Kavakiotis, Ioannis Miliotis, Marios Koussounadis, Antonis Karagkouni, Dimitra Hatzigeorgiou, Artemis G. Genes (Basel) Article microRNAs (miRNAs) are small non-coding RNAs (~22 nts) that are considered central post-transcriptional regulators of gene expression and key components in many pathological conditions. Next-Generation Sequencing (NGS) technologies have led to inexpensive, massive data production, revolutionizing every research aspect in the fields of biology and medicine. Particularly, small RNA-Seq (sRNA-Seq) enables small non-coding RNA quantification on a high-throughput scale, providing a closer look into the expression profiles of these crucial regulators within the cell. Here, we present DIANA-microRNA-Analysis-Pipeline (DIANA-mAP), a fully automated computational pipeline that allows the user to perform miRNA NGS data analysis from raw sRNA-Seq libraries to quantification and Differential Expression Analysis in an easy, scalable, efficient, and intuitive way. Emphasis has been given to data pre-processing, an early, critical step in the analysis for the robustness of the final results and conclusions. Through modularity, parallelizability and customization, DIANA-mAP produces high quality expression results, reports and graphs for downstream data mining and statistical analysis. In an extended evaluation, the tool outperforms similar tools providing pre-processing without any adapter knowledge. Closing, DIANA-mAP is a freely available tool. It is available dockerized with no dependency installations or standalone, accompanied by an installation manual through Github. MDPI 2020-12-30 /pmc/articles/PMC7823405/ /pubmed/33396959 http://dx.doi.org/10.3390/genes12010046 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Alexiou, Athanasios Zisis, Dimitrios Kavakiotis, Ioannis Miliotis, Marios Koussounadis, Antonis Karagkouni, Dimitra Hatzigeorgiou, Artemis G. DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title | DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title_full | DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title_fullStr | DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title_full_unstemmed | DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title_short | DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification |
title_sort | diana-map: analyzing mirna from raw ngs data to quantification |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823405/ https://www.ncbi.nlm.nih.gov/pubmed/33396959 http://dx.doi.org/10.3390/genes12010046 |
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