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dc.contributor.authorConesa, Anaen
dc.contributor.authorMadrigal, Pedroen
dc.contributor.authorTarazona, Soniaen
dc.contributor.authorGomez-Cabrero, Daviden
dc.contributor.authorCervera, Alejandraen
dc.contributor.authorMcPherson, Andrewen
dc.contributor.authorWojciech, Szcześniak Michałen
dc.contributor.authorGaffney, Danielen
dc.contributor.authorElo, Laura Len
dc.contributor.authorZhang, Xuegongen
dc.contributor.authorMortazavi, Alien
dc.date.accessioned2016-01-13T17:47:10Z
dc.date.available2016-01-13T17:47:10Z
dc.date.issued2016-01-26en
dc.identifier.citationGenome Biology 2016 17:13. DOI: 10.1186/s13059-016-0881-8en
dc.identifier.issn1474-7596
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/253244
dc.description.abstractRNA sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all major steps of RNA-seq data analysis including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
dc.languageEnglishen
dc.language.isoenen
dc.publisherBioMed Central
dc.rightsAttribution 2.0 UK: England & Wales
dc.rightsCreative Commons Attribution License 2.0 UK
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/uk/
dc.subjectRNA-seqen
dc.subjectNext-generation sequencingen
dc.subjecttranscriptomicsen
dc.subjectdifferential gene expressionen
dc.subjectguidelinesen
dc.subjectstandardsen
dc.titleA Survey of Best Practices for RNA-seq Data Analysisen
dc.typeArticle
dc.description.versionThis is the final published version. It first appeared at http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8.en
prism.number13en
prism.publicationDate2016en
prism.volume17en
rioxxterms.versionofrecord10.1186/s13059-016-0881-8en
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2016-01-26en
dc.contributor.orcidMadrigal, Pedro [0000-0003-1959-8199]
dc.identifier.eissn1474-760X
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idMRC (MC_PC_12009)


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Attribution 2.0 UK: England & Wales
Except where otherwise noted, this item's licence is described as Attribution 2.0 UK: England & Wales