Journal article Open Access

A survey of best practices for RNA-seq data analysis

Conesa, Ana; Madrigal, Pedro; Tarazona, Sonia; Gomez-Cabrero, David; Cervera, Alejandra; McPherson, Andrew; Szcześniak, Michał Wojciech; Gaffney, Daniel J.; Elo, Laura L.; Zhang, Xuegong; Mortazavi, Ali


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nam##2200000uu#4500</leader>
  <controlfield tag="005">20191104071119.0</controlfield>
  <controlfield tag="001">59349</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK</subfield>
    <subfield code="a">Madrigal, Pedro</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain</subfield>
    <subfield code="a">Tarazona, Sonia</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 77, Stockholm, Sweden</subfield>
    <subfield code="a">Gomez-Cabrero, David</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, 00014, Helsinki, Finland</subfield>
    <subfield code="a">Cervera, Alejandra</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada</subfield>
    <subfield code="a">McPherson, Andrew</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland</subfield>
    <subfield code="a">Szcześniak, Michał Wojciech</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK</subfield>
    <subfield code="a">Gaffney, Daniel J.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland</subfield>
    <subfield code="a">Elo, Laura L.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Key Lab of Bioinformatics/Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, 100084, China</subfield>
    <subfield code="a">Zhang, Xuegong</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA</subfield>
    <subfield code="a">Mortazavi, Ali</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">1179947</subfield>
    <subfield code="z">md5:ccf37eeea6405b1a51e9e09b9d939262</subfield>
    <subfield code="u">https://zenodo.org/record/59349/files/13059_2016_881_MOESM1_ESM.pdf</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">1122217</subfield>
    <subfield code="z">md5:ba0e6facb307d18f3a7fcab7bbf83bc9</subfield>
    <subfield code="u">https://zenodo.org/record/59349/files/13059_2016_Article_881.pdf</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">29596</subfield>
    <subfield code="z">md5:6eb2ea2742d4fd702de82459bdf20453</subfield>
    <subfield code="u">https://zenodo.org/record/59349/files/13059_2016_Article_881.xml.Meta</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2016-01-26</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">user-fp7-bmc</subfield>
    <subfield code="o">oai:zenodo.org:59349</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="4">
    <subfield code="c">13</subfield>
    <subfield code="n">1</subfield>
    <subfield code="p">Genome Biology</subfield>
    <subfield code="v">17</subfield>
    <subfield code="y">2016</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA</subfield>
    <subfield code="a">Conesa, Ana</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">A survey of best practices for RNA-seq data analysis</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-fp7-bmc</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">http://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in 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 the 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.&lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.1186/s13059-016-0881-8</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">publication</subfield>
    <subfield code="b">article</subfield>
  </datafield>
</record>
15
56
views
downloads
Views 15
Downloads 56
Data volume 63.8 MB
Unique views 15
Unique downloads 54

Share

Cite as