Publication: mirnaQC: a webserver for comparative quality control of miRNA-seq data.
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Identifiers
Date
2020-05-21
Authors
Aparicio-Puerta, Ernesto
Gomez-Martin, Cristina
Giannoukakos, Stavros
Medina, Jose Maria
Marchal, Juan Antonio
Hackenberg, Michael
Advisors
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Abstract
Although miRNA-seq is extensively used in many different fields, its quality control is frequently restricted to a PhredScore-based filter. Other important quality related aspects like microRNA yield, the fraction of putative degradation products (such as rRNA fragments) or the percentage of adapter-dimers are hard to assess using absolute thresholds. Here we present mirnaQC, a webserver that relies on 34 quality parameters to assist in miRNA-seq quality control. To improve their interpretability, quality attributes are ranked using a reference distribution obtained from over 36 000 publicly available miRNA-seq datasets. Accepted input formats include FASTQ and SRA accessions. The results page contains several sections that deal with putative technical artefacts related to library preparation, sequencing, contamination or yield. Different visualisations, including PCA and heatmaps, are available to help users identify underlying issues. Finally, we show the usefulness of this approach by analysing two publicly available datasets and discussing the different quality issues that can be detected using mirnaQC.
Description
MeSH Terms
Artifacts
MicroRNAs
Quality Control
Software
RNA, Ribosomal
MicroRNAs
Quality Control
Software
RNA, Ribosomal
DeCS Terms
ARN Ribosómico
Artefactos
Control de calidad
MicroARNs
Programas informáticos
Artefactos
Control de calidad
MicroARNs
Programas informáticos
CIE Terms
Keywords
Female, Humans, Sequence Analysis, RNA, Uterine Cervical Neoplasms
Citation
Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Marchal JA, Hackenberg M. mirnaQC: a webserver for comparative quality control of miRNA-seq data. Nucleic Acids Res. 2020 Jul 2;48(W1):W262-W267.