Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Alexiou, Athanasios, Zisis, Dimitrios, Kavakiotis, Ioannis, Miliotis, Marios, Koussounadis, Antonis, Karagkouni, Dimitra, Hatzigeorgiou, Artemis G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
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
_version_ 1783639828100808704
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
work_keys_str_mv AT alexiouathanasios dianamapanalyzingmirnafromrawngsdatatoquantification
AT zisisdimitrios dianamapanalyzingmirnafromrawngsdatatoquantification
AT kavakiotisioannis dianamapanalyzingmirnafromrawngsdatatoquantification
AT miliotismarios dianamapanalyzingmirnafromrawngsdatatoquantification
AT koussounadisantonis dianamapanalyzingmirnafromrawngsdatatoquantification
AT karagkounidimitra dianamapanalyzingmirnafromrawngsdatatoquantification
AT hatzigeorgiouartemisg dianamapanalyzingmirnafromrawngsdatatoquantification