{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T17:06:40Z","timestamp":1778000800335,"version":"3.51.4"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T00:00:00Z","timestamp":1591056000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["765492"],"award-info":[{"award-number":["765492"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish Government","award":["AGL2017-88702-C2-2-R]"],"award-info":[{"award-number":["AGL2017-88702-C2-2-R]"]}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","award":["SOMM17-6109"],"award-info":[{"award-number":["SOMM17-6109"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","award":["UCE-PP2017-3"],"award-info":[{"award-number":["UCE-PP2017-3"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","award":["PIE16\/00045"],"award-info":[{"award-number":["PIE16\/00045"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["IFI16\/00041"],"award-info":[{"award-number":["IFI16\/00041"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/nar\/gkaa452","type":"journal-article","created":{"date-parts":[[2020,5,21]],"date-time":"2020-05-21T19:19:05Z","timestamp":1590088745000},"page":"W262-W267","source":"Crossref","is-referenced-by-count":25,"title":["mirnaQC: a webserver for comparative quality control of miRNA-seq data"],"prefix":"10.1093","volume":"48","author":[{"given":"Ernesto","family":"Aparicio-Puerta","sequence":"first","affiliation":[{"name":"Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain"},{"name":"Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigaci\u00f3n Biom\u00e9dica, PTS, Avda. del Conocimiento s\/n, 18100-Granada. Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain"},{"name":"Excellence Research Unit \"Modelling Nature\" (MNat), University of Granada, 18071 Granada, Spain"}]},{"given":"Cristina","family":"G\u00f3mez-Mart\u00edn","sequence":"first","affiliation":[{"name":"Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain"},{"name":"Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigaci\u00f3n Biom\u00e9dica, PTS, Avda. del Conocimiento s\/n, 18100-Granada. Spain"}]},{"given":"Stavros","family":"Giannoukakos","sequence":"first","affiliation":[{"name":"Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain"},{"name":"Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigaci\u00f3n Biom\u00e9dica, PTS, Avda. del Conocimiento s\/n, 18100-Granada. Spain"}]},{"given":"Jos\u00e9\u00a0Mar\u00eda","family":"Medina","sequence":"first","affiliation":[{"name":"Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain"},{"name":"Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigaci\u00f3n Biom\u00e9dica, PTS, Avda. del Conocimiento s\/n, 18100-Granada. Spain"}]},{"given":"Juan Antonio","family":"Marchal","sequence":"first","affiliation":[{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain"},{"name":"Excellence Research Unit \"Modelling Nature\" (MNat), University of Granada, 18071 Granada, Spain"},{"name":"Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, University of Granada, Granada, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2248-3114","authenticated-orcid":false,"given":"Michael","family":"Hackenberg","sequence":"first","affiliation":[{"name":"Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain"},{"name":"Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigaci\u00f3n Biom\u00e9dica, PTS, Avda. del Conocimiento s\/n, 18100-Granada. Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain"},{"name":"Excellence Research Unit \"Modelling Nature\" (MNat), University of Granada, 18071 Granada, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,6,2]]},"reference":[{"key":"2020062614045418200_B1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1758-907X-3-4","article-title":"Reducing ligation bias of small RNAs in libraries for next generation sequencing","volume":"3","author":"Sorefan","year":"2012","journal-title":"Silence"},{"key":"2020062614045418200_B2","doi-asserted-by":"crossref","first-page":"731479","DOI":"10.1155\/2015\/731479","article-title":"Challenges in using circulating miRNAs as cancer biomarkers","volume":"2015","author":"Tiberio","year":"2015","journal-title":"Biomed Res. 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