{"data":{"id":"10.6084/m9.figshare.707354","type":"dois","attributes":{"doi":"10.6084/m9.figshare.707354","prefix":"10.6084","suffix":"m9.figshare.707354","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Dunn, Augustine","nameType":"Personal","givenName":"Augustine","familyName":"Dunn","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Diagram of Abbreviated Tophat/Cufflinks Inputs and Outputs"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[],"dates":[{"date":"2013-05-29","dateType":"Created"},{"date":"2015-12-02","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["2270233 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"This figure demonstrates the complexities of a typical RNA-seq experiment as analyzed with the \"Tuxedo Protocol\". It models a fairly simple two condition experiment with each condition having three replications. It is \"abbreviated\" in that it only displays the output files that will be used in the next step for all steps except the 'cuffdiff' step. The complete output of 'cuffdiff' is included to demonstrate the final challenge of integrating the data which exists in multiple cross-referenced files. Colors: \u003cstrong\u003eDark Blue\u003c/strong\u003e - Inputs/Outputs associated with Condition Zero \u003cstrong\u003eLight Blue\u003c/strong\u003e - Inputs/Outputs associated with Condition One \u003cstrong\u003eGrey\u003c/strong\u003e - Inputs/Outputs associated with Condition Zero AND Condition One \u003cstrong\u003eGreen\u003c/strong\u003e - Inputs Specific to the Reference Genome \u003cstrong\u003eGold\u003c/strong\u003e - Program Calls","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Diagram_of_Abbreviated_Tophat_Cufflinks_Inputs_and_Outputs/707354","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":0,"citationCount":0,"citationsOverTime":[],"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2013-05-29T01:03:31.000Z","registered":"2013-05-29T01:03:32.000Z","published":"2013","updated":"2020-09-05T01:56:05.000Z"},"relationships":{"client":{"data":{"id":"figshare.ars","type":"clients"}},"provider":{"data":{"id":"otjm","type":"providers"}},"media":{"data":{"id":"10.6084/m9.figshare.707354","type":"media"}},"references":{"data":[]},"citations":{"data":[]},"parts":{"data":[]},"partOf":{"data":[]},"versions":{"data":[]},"versionOf":{"data":[]}}}}