Publication:
mirnaQC: a webserver for comparative quality control of miRNA-seq data.

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Date

2020-05-21

Authors

Aparicio-Puerta, Ernesto
Gomez-Martin, Cristina
Giannoukakos, Stavros
Medina, Jose Maria
Marchal, Juan Antonio
Hackenberg, Michael

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Oxford University Press
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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.

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MeSH Terms

Artifacts
MicroRNAs
Quality Control
Software
RNA, Ribosomal

DeCS Terms

ARN Ribosómico
Artefactos
Control de calidad
MicroARNs
Programas informáticos

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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.