mirnaQC: a webserver for comparative quality control of miRNA-seq data
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AuthorAparicio Puerta, Ernesto; Gómez Martín, Cristina; Giannoukakos, Stavros; Medina Muñoz, José María
Oxford University Press
Aparicio-Puerta, E., Gómez-Martín, C., Giannoukakos, S., Medina, J. M., Marchal, J. A., & Hackenberg, M. (2020). mirnaQC: a webserver for comparative quality control of miRNA-seq data. Nucleic Acids Research. [doi: 10.1093/nar/gkaa452]
SponsorshipEuropean Union (EU) 765492; Spanish Government AGL2017-88702-C2-2-R; Junta de Andalucia; European Union (EU) 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
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 availablemiRNA-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.