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ASE is detectable by differential expression analysis (DEA) applied to the counts of RNA-seq read pairs aligned to parental references, but aligners do not always choose the correct parental reference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We used public data for species that are known to hybridize. We measured our ability to assign RNA-seq read pairs to their proper transcriptome or genome references. We tested software packages that assign each read pair to a reference position and found that they often favored the incorrect species reference. To address this problem, we introduce a post process that extracts alignment features and trains a random forest classifier to choose the better alignment. On each simulated hybrid dataset tested, our machine-learning post-processor achieved higher accuracy than the aligner by itself at choosing the correct parent-of-origin per RNA-seq read pair.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>For the parent-of-origin classification of RNA-seq, machine learning can improve the accuracy of alignment-based methods. This approach could be useful for enhancing ASE detection in interspecies hybrids, though RNA-seq from real hybrids may present challenges not captured by our simulations. We believe this is the first application of machine learning to this problem domain.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-024-05728-3","type":"journal-article","created":{"date-parts":[[2024,3,12]],"date-time":"2024-03-12T04:02:03Z","timestamp":1710216123000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6912-2925","authenticated-orcid":false,"given":"Jason R.","family":"Miller","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7982-4744","authenticated-orcid":false,"given":"Donald A.","family":"Adjeroh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2024,3,12]]},"reference":[{"issue":"11","key":"5728_CR1","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","volume":"20","author":"R Stark","year":"2019","unstructured":"Stark R, Grzelak M, Hadfield J. 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