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2020-12-10Zeitschriftenartikel DOI: 10.3390/genes11121487
RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow
dc.contributor.authorLataretu, Marie
dc.contributor.authorHölzer, Martin
dc.date.accessioned2021-02-09T11:44:47Z
dc.date.available2021-02-09T11:44:47Z
dc.date.issued2020-12-10none
dc.identifier.other10.3390/genes11121487
dc.identifier.urihttp://edoc.rki.de/176904/7762
dc.description.abstractRNA-Seq enables the identification and quantification of RNA molecules, often with the aim of detecting differentially expressed genes (DEGs). Although RNA-Seq evolved into a standard technique, there is no universal gold standard for these data’s computational analysis. On top of that, previous studies proved the irreproducibility of RNA-Seq studies. Here, we present a portable, scalable, and parallelizable Nextflow RNA-Seq pipeline to detect DEGs, which assures a high level of reproducibility. The pipeline automatically takes care of common pitfalls, such as ribosomal RNA removal and low abundance gene filtering. Apart from various visualizations for the DEG results, we incorporated downstream pathway analysis for common species as Homo sapiens and Mus musculus. We evaluated the DEG detection functionality while using qRT-PCR data serving as a reference and observed a very high correlation of the logarithmized gene expression fold changes.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectRNA-Seqeng
dc.subjectworkfloweng
dc.subjectNextflow pipelineeng
dc.subjectdifferential gene expression analysiseng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleRNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflownone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/7762-9
dc.identifier.doihttps://doi.org/10.3390/genes11121487
dc.identifier.doihttp://dx.doi.org/10.25646/7984
dc.type.versionpublishedVersionnone
local.edoc.container-titlegenesnone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.mdpi.com/2073-4425/11/12/1487none
local.edoc.container-publisher-nameMDPInone
local.edoc.container-volume11none
local.edoc.container-issue12none
local.edoc.container-reportyear2020none
local.edoc.container-firstpage1none
local.edoc.container-lastpage17none
local.edoc.rki-departmentMethodenentwicklung und Forschungsinfrastrukturnone
dc.description.versionPeer Reviewednone

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