Journal
NUCLEIC ACIDS RESEARCH
Volume 48, Issue W1, Pages W262-W267Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa452
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Funding
- European Union [765492]
- Spanish Government [AGL2017-88702-C2-2-R]
- Consejeria de Economia, Conocimiento, Empresas y Universidad de la Junta de Andalucia
- European Regional Development Funds (ERDF) [SOMM17-6109, UCE-PP2017-3]
- Instituto de Salud Carlos III, ERDF funds [PIE16/00045]
- Instituto de Salud Carlos III [IFI16/00041]
- Chair 'Doctors Galera-Requena in cancer stem cell research'
- Excellence Research Unit Modelling Nature (MNat) [SOMM17-6109]
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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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