{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T21:13:54Z","timestamp":1768511634467,"version":"3.49.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not. With the compilation of large-scale RNA-Seq datasets with technical replicate samples, however, we can now, for the first time, perform a systematic analysis of the precision of expression level estimates from massively parallel sequencing technology. This then allows considerations for its improvement by computational or experimental means.<\/jats:p>\n               <jats:p>Results: We report on a comprehensive study of target identification and measurement precision, including their dependence on transcript expression levels, read depth and other parameters. In particular, an impressive recall of 84% of the estimated true transcript population could be achieved with 331 million 50 bp reads, with diminishing returns from longer read lengths and even less gains from increased sequencing depths. Most of the measurement power (75%) is spent on only 7% of the known transcriptome, however, making less strongly expressed transcripts harder to measure. Consequently, &amp;lt;30% of all transcripts could be quantified reliably with a relative error &amp;lt;20%. Based on established tools, we then introduce a new approach for mapping and analysing sequencing reads that yields substantially improved performance in gene expression profiling, increasing the number of transcripts that can reliably be quantified to over 40%. Extrapolations to higher sequencing depths highlight the need for efficient complementary steps. In discussion we outline possible experimental and computational strategies for further improvements in quantification precision.<\/jats:p>\n               <jats:p>Contact: \u00a0rnaseq10@boku.ac.at<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr247","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i383-i391","source":"Crossref","is-referenced-by-count":121,"title":["Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling"],"prefix":"10.1093","volume":"27","author":[{"given":"Pawe\u0142 P.","family":"\u0141abaj","sequence":"first","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]},{"given":"Germ\u00e1n G.","family":"Leparc","sequence":"additional","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]},{"given":"Bryan E.","family":"Linggi","sequence":"additional","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]},{"given":"Lye Meng","family":"Markillie","sequence":"additional","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]},{"given":"H. Steven","family":"Wiley","sequence":"additional","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]},{"given":"David P.","family":"Kreil","sequence":"additional","affiliation":[{"name":"1 Chair of Bioinformatics, Boku University Vienna, 1190 Muthgasse 18, Vienna, Austria and 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512160992000_B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512160992000_B2","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1073\/pnas.86.4.1249","article-title":"Distinctive traits of normal and tumor-derived human mammary epithelial cells expressed in a medium that supports long-term growth of both cell types","volume":"86","author":"Band","year":"1989","journal-title":"Proc. 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