{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T03:40:50Z","timestamp":1770349250654,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,12,9]],"date-time":"2019-12-09T00:00:00Z","timestamp":1575849600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Centre de Recherche du Centre Hospitalier de l\u2019Universit\u00e9 de Sherbrooke"},{"name":"Fonds de Recherche du Qu\u00e9bec\u2014Sant\u00e9"},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2018-05412"],"award-info":[{"award-number":["RGPIN-2018-05412"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Ribonucleic acid sequencing (RNA-seq) identifies and quantifies RNA molecules from a biological sample. Transformation from raw sequencing data to meaningful gene or isoform counts requires an in silico bioinformatics pipeline. Such pipelines are modular in nature, built using selected software and biological references. Software is usually chosen and parameterized according to the sequencing protocol and biological question. However, while biological and technical noise is alleviated through replicates, biases due to the pipeline and choice of biological references are often overlooked. Here, we show that the current standard practice prevents reproducibility in RNA-seq studies by failing to specify required methodological information. Peer-reviewed articles are intended to apply currently accepted scientific and methodological standards. Inasmuch as the bias-less and optimal RNA-seq pipeline is not perfectly defined, methodological information holds a meaningful role in defining the results. This work illustrates the need for a standardized and explicit display of methodological information in RNA-seq experiments.<\/jats:p>","DOI":"10.1093\/bib\/bbz124","type":"journal-article","created":{"date-parts":[[2019,9,4]],"date-time":"2019-09-04T19:26:49Z","timestamp":1567625209000},"page":"140-145","source":"Crossref","is-referenced-by-count":77,"title":["Current RNA-seq methodology reporting limits reproducibility"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1825-7157","authenticated-orcid":false,"given":"Jo\u00ebl","family":"Simoneau","sequence":"first","affiliation":[{"name":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"}]},{"given":"Simon","family":"Dumontier","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"}]},{"given":"Ryan","family":"Gosselin","sequence":"additional","affiliation":[{"name":"Department of Chemical & Biotechnological Engineering, Faculty of Engineering, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6231-7714","authenticated-orcid":false,"given":"Michelle S","family":"Scott","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Faculty of Medicine and Health Sciences, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"}]}],"member":"286","published-online":{"date-parts":[[2019,12,10]]},"reference":[{"key":"2021012203302026400_ref1","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1126\/science.270.5235.467","article-title":"Quantitative monitoring of gene expression patterns with a complementary DNA 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