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However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>At both the transcript and gene levels, 2\u2009\u00d7\u200940 paired-end reads unequivocally provide expression estimates that are more highly correlated with 2\u2009\u00d7\u2009125 than 1\u2009\u00d7\u200975 reads; in nearly all cases, those correlations are also greater than for 1\u2009\u00d7\u2009125, despite the greater total number of sequenced bases for the latter. Across an array of metrics, differential expression tests based upon 2\u2009\u00d7\u200940 consistently outperform those using 1\u2009\u00d7\u200975.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Researchers seeking a cost-effective approach for gene-level expression analysis should prefer short paired-end reads over a longer single-end strategy. Short paired-end reads will also give reasonably robust expression estimates and differential expression results at the isoform level.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-020-3484-z","type":"journal-article","created":{"date-parts":[[2020,4,19]],"date-time":"2020-04-19T09:02:21Z","timestamp":1587286941000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["Short paired-end reads trump long single-end reads for expression analysis"],"prefix":"10.1186","volume":"21","author":[{"given":"Adam H.","family":"Freedman","sequence":"first","affiliation":[]},{"given":"John M.","family":"Gaspar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1673-9216","authenticated-orcid":false,"given":"Timothy B.","family":"Sackton","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,4,19]]},"reference":[{"issue":"7369","key":"3484_CR1","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nature10532","volume":"478","author":"D Brawand","year":"2011","unstructured":"Brawand D, Soumillon M, Necsulea A, Julien P, Cs\u00e1rdi G, Harrigan P, et al. 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