mirnaQC: a webserver for comparative quality control of miRNA-seq data release_elqok5hfezgsvpahdpcomdsmiq

by Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Juan Antonio Marchal, Michael Hackenberg

Published in Nucleic Acids Research by Oxford University Press (OUP).

2020  

Abstract

<jats:title>Abstract</jats:title> 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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Type  article-journal
Stage   published
Date   2020-06-02
Language   en ?
DOI  10.1093/nar/gkaa452
PubMed  32484556
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