{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1363670318208563200.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1038/s41467-017-00050-4"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/s41467-017-00050-4.pdf"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/s41467-017-00050-4"}}],"dc:title":[{"@value":"Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title><jats:p>RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to unleash the power within RNA-seq. Here we conduct an extensive study analysing a broad spectrum of RNA-seq workflows. Surpassing the expression analysis scope, our work also includes assessment of RNA variant-calling, RNA editing and RNA fusion detection techniques. Specifically, we examine both short- and long-read RNA-seq technologies, 39 analysis tools resulting in ~120 combinations, and ~490 analyses involving 15 samples with a variety of germline, cancer and stem cell data sets. We report the performance and propose a comprehensive RNA-seq analysis protocol, named RNACocktail, along with a computational pipeline achieving high accuracy. Validation on different samples reveals that our proposed protocol could help researchers extract more biologically relevant predictions by broad analysis of the transcriptome.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1383670318208563075","@type":"Researcher","foaf:name":[{"@value":"Sayed Mohammad Ebrahim Sahraeian"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563076","@type":"Researcher","foaf:name":[{"@value":"Marghoob Mohiyuddin"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563205","@type":"Researcher","foaf:name":[{"@value":"Robert Sebra"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563073","@type":"Researcher","foaf:name":[{"@value":"Hagen Tilgner"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563072","@type":"Researcher","foaf:name":[{"@value":"Pegah T. Afshar"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563202","@type":"Researcher","foaf:name":[{"@value":"Kin Fai Au"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563074","@type":"Researcher","foaf:name":[{"@value":"Narges Bani Asadi"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563204","@type":"Researcher","foaf:name":[{"@value":"Mark B. Gerstein"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563201","@type":"Researcher","foaf:name":[{"@value":"Wing Hung Wong"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563203","@type":"Researcher","foaf:name":[{"@value":"Michael P. Snyder"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563077","@type":"Researcher","foaf:name":[{"@value":"Eric Schadt"}]},{"@id":"https://cir.nii.ac.jp/crid/1383670318208563200","@type":"Researcher","foaf:name":[{"@value":"Hugo Y. K. Lam"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"20411723"}],"prism:publicationName":[{"@value":"Nature Communications"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2017-07-05","prism:volume":"8","prism:number":"1","prism:startingPage":"59"},"reviewed":"false","dc:rights":["https://creativecommons.org/licenses/by/4.0","https://creativecommons.org/licenses/by/4.0"],"url":[{"@id":"https://www.nature.com/articles/s41467-017-00050-4.pdf"},{"@id":"https://www.nature.com/articles/s41467-017-00050-4"}],"createdAt":"2017-06-28","modifiedAt":"2024-06-25","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1360004231894636288","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genome-Wide Scanning of Gene Expression"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021390583651072","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Canine diffuse large B-cell lymphoma downregulates the activity of CD8 + T-cells through tumor-derived extracellular vesicles"}]},{"@id":"https://cir.nii.ac.jp/crid/1360294643709916288","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Impact of human gene annotations on RNA-seq differential expression analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1361131417267295488","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Exploring the selective vulnerability in Alzheimer disease using tissue specific variant analysis"}]},{"@id":"https://cir.nii.ac.jp/crid/1361975842197468160","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Identifying suitable tools for variant detection and differential gene expression using RNA-seq data"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1038/s41467-017-00050-4"},{"@type":"CROSSREF","@value":"10.1016/b978-0-12-809633-8.20132-5_references_DOI_JeXqfYLLeWC9Z7epzdMV2fmirZD"},{"@type":"CROSSREF","@value":"10.1186/s12935-023-03104-4_references_DOI_JeXqfYLLeWC9Z7epzdMV2fmirZD"},{"@type":"CROSSREF","@value":"10.1186/s12864-021-08038-7_references_DOI_JeXqfYLLeWC9Z7epzdMV2fmirZD"},{"@type":"CROSSREF","@value":"10.1016/j.ygeno.2018.05.024_references_DOI_JeXqfYLLeWC9Z7epzdMV2fmirZD"},{"@type":"CROSSREF","@value":"10.1016/j.ygeno.2019.12.011_references_DOI_JeXqfYLLeWC9Z7epzdMV2fmirZD"}]}