{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T13:12:16Z","timestamp":1766754736935,"version":"3.41.2"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T00:00:00Z","timestamp":1727308800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA sequencing is the gold-standard method to quantify transcriptomic changes between two conditions. The overwhelming majority of data analysis methods available are focused on polyadenylated RNA transcribed from single-copy genes and overlook transcripts from repeated sequences such as transposable elements (TEs). These self-autonomous genetic elements are increasingly studied, and specialized tools designed to handle multimapping sequencing reads are available. Transfer RNAs are transcribed by RNA polymerase III and are essential for protein translation. There is a need for integrated software that is able to analyze multiple types of RNA. Here, we present 3t-seq, a Snakemake pipeline for integrated differential expression analysis of transcripts from single-copy genes, TEs, and tRNA. 3t-seq produces an accessible report and easy-to-use results for downstream analysis starting from raw sequencing data and performing quality control, genome mapping, gene expression quantification, and statistical testing. It implements three methods to quantify TEs expression and one for tRNA genes. It provides an easy-to-configure method to manage software dependencies that lets the user focus on results. 3t-seq is released under MIT license and is available at https:\/\/github.com\/boulardlab\/3t-seq<\/jats:p>","DOI":"10.1093\/bib\/bbae467","type":"journal-article","created":{"date-parts":[[2024,9,26]],"date-time":"2024-09-26T01:27:47Z","timestamp":1727314067000},"source":"Crossref","is-referenced-by-count":1,"title":["3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5135-8529","authenticated-orcid":false,"given":"Francesco","family":"Tabaro","sequence":"first","affiliation":[{"name":"Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,","place":["Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7559-5585","authenticated-orcid":false,"given":"Matthieu","family":"Boulard","sequence":"additional","affiliation":[{"name":"Epigenetics and Neurobiology Unit, EMBL Rome, European Molecular Biology Laboratory , Via Ercole Ramarini 32, Monterotondo 00015,","place":["Italy"]}]}],"member":"286","published-online":{"date-parts":[[2024,9,25]]},"reference":[{"key":"2024092601274002900_ref1","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s13059-016-0881-8","article-title":"A survey of best practices for RNA-seq data analysis","volume":"17","author":"Conesa","year":"2016","journal-title":"Genome Biol"},{"key":"2024092601274002900_ref2","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: the teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat Rev Genet"},{"volume-title":"The ENCODE Uniform Analysis Pipelines","author":"Hitz","key":"2024092601274002900_ref3"},{"key":"2024092601274002900_ref4","doi-asserted-by":"publisher","first-page":"102361","DOI":"10.1016\/j.isci.2021.102361","article-title":"NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data","volume":"24","author":"Overbey","year":"2021","journal-title":"iScience"},{"key":"2024092601274002900_ref5","unstructured":"Krueger F, James F, Ewels P. et\u00a0al. FelixKrueger\/TrimGalore: v0.6.10 - add default decompression path (0.6.10). 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