Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
Identifieur interne : 000115 ( Pmc/Checkpoint ); précédent : 000114; suivant : 000116Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data
Auteurs : Mikhail G. Dozmorov [États-Unis] ; Indra Adrianto [États-Unis] ; Cory B. Giles [États-Unis] ; Edmund Glass [États-Unis] ; Stuart B. Glenn [États-Unis] ; Courtney Montgomery [États-Unis] ; Kathy L. Sivils [États-Unis] ; Lorin E. Olson [États-Unis] ; Tomoaki Iwayama [États-Unis] ; Willard M. Freeman [États-Unis] ; Christopher J. Lessard [États-Unis] ; Jonathan D. Wren [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2015.
Abstract
Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problematic for accurate assessment of the biological signal, yet their impact on sequencing data has not received much attention. We investigate how trimming the adapters, removing duplicates, and filtering out reads overlapping low complexity regions influence the significance of biological signal in RNA- and ChIP-seq experiments.
We assessed the effect of data processing steps on the alignment statistics and the functional enrichment analysis results of RNA- and ChIP-seq data. We compared differentially processed RNA-seq data with matching microarray data on the same patient samples to determine whether changes in pre-processing improved correlation between the two. We have developed a simple tool to remove low complexity regions, RepeatSoaker, available at
Both adapter trimming and duplicate removal moderately improved the strength of biological signals in RNA-seq and ChIP-seq data. Aggressive filtering of reads overlapping with low complexity regions, as defined by RepeatMasker, further improved the strength of biological signals, and the correlation between RNA-seq and microarray gene expression data.
Adapter trimming and duplicates removal, coupled with filtering out reads overlapping low complexity regions, is shown to increase the quality and reliability of detecting biological signals in RNA-seq and ChIP-seq data.
Url:
DOI: 10.1186/1471-2105-16-S13-S10
PubMed: 26423047
PubMed Central: 4597324
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:4597324Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data</title>
<author><name sortKey="Dozmorov, Mikhail G" sort="Dozmorov, Mikhail G" uniqKey="Dozmorov M" first="Mikhail G" last="Dozmorov">Mikhail G. Dozmorov</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biostatistics, Virginia Commonwealth University, Richmond, VA</wicri:regionArea>
<placeName><region type="state">Virginie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Adrianto, Indra" sort="Adrianto, Indra" uniqKey="Adrianto I" first="Indra" last="Adrianto">Indra Adrianto</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Giles, Cory B" sort="Giles, Cory B" uniqKey="Giles C" first="Cory B" last="Giles">Cory B. Giles</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Glass, Edmund" sort="Glass, Edmund" uniqKey="Glass E" first="Edmund" last="Glass">Edmund Glass</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biostatistics, Virginia Commonwealth University, Richmond, VA</wicri:regionArea>
<placeName><region type="state">Virginie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Glenn, Stuart B" sort="Glenn, Stuart B" uniqKey="Glenn S" first="Stuart B" last="Glenn">Stuart B. Glenn</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Montgomery, Courtney" sort="Montgomery, Courtney" uniqKey="Montgomery C" first="Courtney" last="Montgomery">Courtney Montgomery</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sivils, Kathy L" sort="Sivils, Kathy L" uniqKey="Sivils K" first="Kathy L" last="Sivils">Kathy L. Sivils</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Olson, Lorin E" sort="Olson, Lorin E" uniqKey="Olson L" first="Lorin E" last="Olson">Lorin E. Olson</name>
<affiliation wicri:level="2"><nlm:aff id="I3">Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Iwayama, Tomoaki" sort="Iwayama, Tomoaki" uniqKey="Iwayama T" first="Tomoaki" last="Iwayama">Tomoaki Iwayama</name>
<affiliation wicri:level="2"><nlm:aff id="I3">Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Freeman, Willard M" sort="Freeman, Willard M" uniqKey="Freeman W" first="Willard M" last="Freeman">Willard M. Freeman</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I5">Department of Physiology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Physiology, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lessard, Christopher J" sort="Lessard, Christopher J" uniqKey="Lessard C" first="Christopher J" last="Lessard">Christopher J. Lessard</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wren, Jonathan D" sort="Wren, Jonathan D" uniqKey="Wren J" first="Jonathan D" last="Wren">Jonathan D. Wren</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">26423047</idno>
<idno type="pmc">4597324</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597324</idno>
<idno type="RBID">PMC:4597324</idno>
<idno type="doi">10.1186/1471-2105-16-S13-S10</idno>
<date when="2015">2015</date>
<idno type="wicri:Area/Pmc/Corpus">000227</idno>
<idno type="wicri:Area/Pmc/Curation">000227</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000115</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data</title>
<author><name sortKey="Dozmorov, Mikhail G" sort="Dozmorov, Mikhail G" uniqKey="Dozmorov M" first="Mikhail G" last="Dozmorov">Mikhail G. Dozmorov</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biostatistics, Virginia Commonwealth University, Richmond, VA</wicri:regionArea>
<placeName><region type="state">Virginie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Adrianto, Indra" sort="Adrianto, Indra" uniqKey="Adrianto I" first="Indra" last="Adrianto">Indra Adrianto</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Giles, Cory B" sort="Giles, Cory B" uniqKey="Giles C" first="Cory B" last="Giles">Cory B. Giles</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Glass, Edmund" sort="Glass, Edmund" uniqKey="Glass E" first="Edmund" last="Glass">Edmund Glass</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biostatistics, Virginia Commonwealth University, Richmond, VA</wicri:regionArea>
<placeName><region type="state">Virginie</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Glenn, Stuart B" sort="Glenn, Stuart B" uniqKey="Glenn S" first="Stuart B" last="Glenn">Stuart B. Glenn</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Montgomery, Courtney" sort="Montgomery, Courtney" uniqKey="Montgomery C" first="Courtney" last="Montgomery">Courtney Montgomery</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Sivils, Kathy L" sort="Sivils, Kathy L" uniqKey="Sivils K" first="Kathy L" last="Sivils">Kathy L. Sivils</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Olson, Lorin E" sort="Olson, Lorin E" uniqKey="Olson L" first="Lorin E" last="Olson">Lorin E. Olson</name>
<affiliation wicri:level="2"><nlm:aff id="I3">Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Iwayama, Tomoaki" sort="Iwayama, Tomoaki" uniqKey="Iwayama T" first="Tomoaki" last="Iwayama">Tomoaki Iwayama</name>
<affiliation wicri:level="2"><nlm:aff id="I3">Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Freeman, Willard M" sort="Freeman, Willard M" uniqKey="Freeman W" first="Willard M" last="Freeman">Willard M. Freeman</name>
<affiliation wicri:level="2"><nlm:aff id="I4">Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I5">Department of Physiology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Physiology, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lessard, Christopher J" sort="Lessard, Christopher J" uniqKey="Lessard C" first="Christopher J" last="Lessard">Christopher J. Lessard</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wren, Jonathan D" sort="Wren, Jonathan D" uniqKey="Wren J" first="Jonathan D" last="Wren">Jonathan D. Wren</name>
<affiliation wicri:level="2"><nlm:aff id="I2">Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><nlm:aff id="I6">Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center. Oklahoma City, OK</wicri:regionArea>
<placeName><region type="state">Oklahoma</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problematic for accurate assessment of the biological signal, yet their impact on sequencing data has not received much attention. We investigate how trimming the adapters, removing duplicates, and filtering out reads overlapping low complexity regions influence the significance of biological signal in RNA- and ChIP-seq experiments.</p>
</sec>
<sec><title>Methods</title>
<p>We assessed the effect of data processing steps on the alignment statistics and the functional enrichment analysis results of RNA- and ChIP-seq data. We compared differentially processed RNA-seq data with matching microarray data on the same patient samples to determine whether changes in pre-processing improved correlation between the two. We have developed a simple tool to remove low complexity regions, RepeatSoaker, available at <ext-link ext-link-type="uri" xlink:href="https://github.com/mdozmorov/RepeatSoaker">https://github.com/mdozmorov/RepeatSoaker</ext-link>
, and tested its effect on the alignment statistics and the results of the enrichment analyses.</p>
</sec>
<sec><title>Results</title>
<p>Both adapter trimming and duplicate removal moderately improved the strength of biological signals in RNA-seq and ChIP-seq data. Aggressive filtering of reads overlapping with low complexity regions, as defined by RepeatMasker, further improved the strength of biological signals, and the correlation between RNA-seq and microarray gene expression data.</p>
</sec>
<sec><title>Conclusions</title>
<p>Adapter trimming and duplicates removal, coupled with filtering out reads overlapping low complexity regions, is shown to increase the quality and reliability of detecting biological signals in RNA-seq and ChIP-seq data.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Huddleston, J" uniqKey="Huddleston J">J Huddleston</name>
</author>
<author><name sortKey="Ranade, S" uniqKey="Ranade S">S Ranade</name>
</author>
<author><name sortKey="Malig, M" uniqKey="Malig M">M Malig</name>
</author>
<author><name sortKey="Antonacci, F" uniqKey="Antonacci F">F Antonacci</name>
</author>
<author><name sortKey="Chaisson, M" uniqKey="Chaisson M">M Chaisson</name>
</author>
<author><name sortKey="Hon, L" uniqKey="Hon L">L Hon</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Howorka, S" uniqKey="Howorka S">S Howorka</name>
</author>
<author><name sortKey="Cheley, S" uniqKey="Cheley S">S Cheley</name>
</author>
<author><name sortKey="Bayley, H" uniqKey="Bayley H">H Bayley</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Walsh, P" uniqKey="Walsh P">P Walsh</name>
</author>
<author><name sortKey="Lu, X" uniqKey="Lu X">X Lu</name>
</author>
<author><name sortKey="Carroll, J" uniqKey="Carroll J">J Carroll</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Del Fabbro, C" uniqKey="Del Fabbro C">C Del Fabbro</name>
</author>
<author><name sortKey="Scalabrin, S" uniqKey="Scalabrin S">S Scalabrin</name>
</author>
<author><name sortKey="Morgante, M" uniqKey="Morgante M">M Morgante</name>
</author>
<author><name sortKey="Giorgi, Fm" uniqKey="Giorgi F">FM Giorgi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Turner, S" uniqKey="Turner S">S Turner</name>
</author>
<author><name sortKey="Armstrong, Ll" uniqKey="Armstrong L">LL Armstrong</name>
</author>
<author><name sortKey="Bradford, Y" uniqKey="Bradford Y">Y Bradford</name>
</author>
<author><name sortKey="Carlson, Cs" uniqKey="Carlson C">CS Carlson</name>
</author>
<author><name sortKey="Crawford, Dc" uniqKey="Crawford D">DC Crawford</name>
</author>
<author><name sortKey="Crenshaw, At" uniqKey="Crenshaw A">AT Crenshaw</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA DePristo</name>
</author>
<author><name sortKey="Banks, E" uniqKey="Banks E">E Banks</name>
</author>
<author><name sortKey="Poplin, R" uniqKey="Poplin R">R Poplin</name>
</author>
<author><name sortKey="Garimella, Kv" uniqKey="Garimella K">KV Garimella</name>
</author>
<author><name sortKey="Maguire, Jr" uniqKey="Maguire J">JR Maguire</name>
</author>
<author><name sortKey="Hartl, C" uniqKey="Hartl C">C Hartl</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Abel, Hj" uniqKey="Abel H">HJ Abel</name>
</author>
<author><name sortKey="Al Kateb, H" uniqKey="Al Kateb H">H Al-Kateb</name>
</author>
<author><name sortKey="Cottrell, Ce" uniqKey="Cottrell C">CE Cottrell</name>
</author>
<author><name sortKey="Bredemeyer, Aj" uniqKey="Bredemeyer A">AJ Bredemeyer</name>
</author>
<author><name sortKey="Pritchard, Cc" uniqKey="Pritchard C">CC Pritchard</name>
</author>
<author><name sortKey="Grossmann, Ah" uniqKey="Grossmann A">AH Grossmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, Y" uniqKey="Chen Y">Y Chen</name>
</author>
<author><name sortKey="Negre, N" uniqKey="Negre N">N Negre</name>
</author>
<author><name sortKey="Li, Q" uniqKey="Li Q">Q Li</name>
</author>
<author><name sortKey="Mieczkowska, Jo" uniqKey="Mieczkowska J">JO Mieczkowska</name>
</author>
<author><name sortKey="Slattery, M" uniqKey="Slattery M">M Slattery</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Handsaker, B" uniqKey="Handsaker B">B Handsaker</name>
</author>
<author><name sortKey="Wysoker, A" uniqKey="Wysoker A">A Wysoker</name>
</author>
<author><name sortKey="Fennell, T" uniqKey="Fennell T">T Fennell</name>
</author>
<author><name sortKey="Ruan, J" uniqKey="Ruan J">J Ruan</name>
</author>
<author><name sortKey="Homer, N" uniqKey="Homer N">N Homer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhou, W" uniqKey="Zhou W">W Zhou</name>
</author>
<author><name sortKey="Chen, T" uniqKey="Chen T">T Chen</name>
</author>
<author><name sortKey="Zhao, H" uniqKey="Zhao H">H Zhao</name>
</author>
<author><name sortKey="Eterovic, Ak" uniqKey="Eterovic A">AK Eterovic</name>
</author>
<author><name sortKey="Meric Bernstam, F" uniqKey="Meric Bernstam F">F Meric-Bernstam</name>
</author>
<author><name sortKey="Mills, Gb" uniqKey="Mills G">GB Mills</name>
</author>
<author><name sortKey="Chen, K" uniqKey="Chen K">K Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Majewski, J" uniqKey="Majewski J">J Majewski</name>
</author>
<author><name sortKey="Ott, J" uniqKey="Ott J">J Ott</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA DePristo</name>
</author>
<author><name sortKey="Zilversmit, Mm" uniqKey="Zilversmit M">MM Zilversmit</name>
</author>
<author><name sortKey="Hartl, Dl" uniqKey="Hartl D">DL Hartl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kapitonov, Vv" uniqKey="Kapitonov V">VV Kapitonov</name>
</author>
<author><name sortKey="Jurka, J" uniqKey="Jurka J">J Jurka</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Li, B" uniqKey="Li B">B Li</name>
</author>
<author><name sortKey="Ruotti, V" uniqKey="Ruotti V">V Ruotti</name>
</author>
<author><name sortKey="Stewart, Rm" uniqKey="Stewart R">RM Stewart</name>
</author>
<author><name sortKey="Thomson, Ja" uniqKey="Thomson J">JA Thomson</name>
</author>
<author><name sortKey="Dewey, Cn" uniqKey="Dewey C">CN Dewey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chung, D" uniqKey="Chung D">D Chung</name>
</author>
<author><name sortKey="Kuan, Pf" uniqKey="Kuan P">PF Kuan</name>
</author>
<author><name sortKey="Li, B" uniqKey="Li B">B Li</name>
</author>
<author><name sortKey="Sanalkumar, R" uniqKey="Sanalkumar R">R Sanalkumar</name>
</author>
<author><name sortKey="Liang, K" uniqKey="Liang K">K Liang</name>
</author>
<author><name sortKey="Bresnick, Eh" uniqKey="Bresnick E">EH Bresnick</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lander, Es" uniqKey="Lander E">ES Lander</name>
</author>
<author><name sortKey="Linton, Lm" uniqKey="Linton L">LM Linton</name>
</author>
<author><name sortKey="Birren, B" uniqKey="Birren B">B Birren</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name>
</author>
<author><name sortKey="Zody, Mc" uniqKey="Zody M">MC Zody</name>
</author>
<author><name sortKey="Baldwin, J" uniqKey="Baldwin J">J Baldwin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Abecasis, Gr" uniqKey="Abecasis G">GR Abecasis</name>
</author>
<author><name sortKey="Auton, A" uniqKey="Auton A">A Auton</name>
</author>
<author><name sortKey="Brooks, Ld" uniqKey="Brooks L">LD Brooks</name>
</author>
<author><name sortKey="Depristo, Ma" uniqKey="Depristo M">MA DePristo</name>
</author>
<author><name sortKey="Durbin, Rm" uniqKey="Durbin R">RM Durbin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hangauer, Mj" uniqKey="Hangauer M">MJ Hangauer</name>
</author>
<author><name sortKey="Vaughn, Iw" uniqKey="Vaughn I">IW Vaughn</name>
</author>
<author><name sortKey="Mcmanus, Mt" uniqKey="Mcmanus M">MT McManus</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pickrell, Jk" uniqKey="Pickrell J">JK Pickrell</name>
</author>
<author><name sortKey="Gaffney, Dj" uniqKey="Gaffney D">DJ Gaffney</name>
</author>
<author><name sortKey="Gilad, Y" uniqKey="Gilad Y">Y Gilad</name>
</author>
<author><name sortKey="Pritchard, Jk" uniqKey="Pritchard J">JK Pritchard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Medvedev, P" uniqKey="Medvedev P">P Medvedev</name>
</author>
<author><name sortKey="Stanciu, M" uniqKey="Stanciu M">M Stanciu</name>
</author>
<author><name sortKey="Brudno, M" uniqKey="Brudno M">M Brudno</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lee, H" uniqKey="Lee H">H Lee</name>
</author>
<author><name sortKey="Popodi, E" uniqKey="Popodi E">E Popodi</name>
</author>
<author><name sortKey="Foster, Pl" uniqKey="Foster P">PL Foster</name>
</author>
<author><name sortKey="Tang, H" uniqKey="Tang H">H Tang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schmieder, R" uniqKey="Schmieder R">R Schmieder</name>
</author>
<author><name sortKey="Edwards, R" uniqKey="Edwards R">R Edwards</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Olson, Le" uniqKey="Olson L">LE Olson</name>
</author>
<author><name sortKey="Soriano, P" uniqKey="Soriano P">P Soriano</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bolger, Am" uniqKey="Bolger A">AM Bolger</name>
</author>
<author><name sortKey="Lohse, M" uniqKey="Lohse M">M Lohse</name>
</author>
<author><name sortKey="Usadel, B" uniqKey="Usadel B">B Usadel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, N" uniqKey="Chen N">N Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name>
</author>
<author><name sortKey="Roberts, A" uniqKey="Roberts A">A Roberts</name>
</author>
<author><name sortKey="Goff, L" uniqKey="Goff L">L Goff</name>
</author>
<author><name sortKey="Pertea, G" uniqKey="Pertea G">G Pertea</name>
</author>
<author><name sortKey="Kim, D" uniqKey="Kim D">D Kim</name>
</author>
<author><name sortKey="Kelley, Dr" uniqKey="Kelley D">DR Kelley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Team, Rdc" uniqKey="Team R">RDC Team</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name>
</author>
<author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name>
</author>
<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Feng, J" uniqKey="Feng J">J Feng</name>
</author>
<author><name sortKey="Liu, T" uniqKey="Liu T">T Liu</name>
</author>
<author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Machanick, P" uniqKey="Machanick P">P Machanick</name>
</author>
<author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rosenbloom, Kr" uniqKey="Rosenbloom K">KR Rosenbloom</name>
</author>
<author><name sortKey="Sloan, Ca" uniqKey="Sloan C">CA Sloan</name>
</author>
<author><name sortKey="Malladi, Vs" uniqKey="Malladi V">VS Malladi</name>
</author>
<author><name sortKey="Dreszer, Tr" uniqKey="Dreszer T">TR Dreszer</name>
</author>
<author><name sortKey="Learned, K" uniqKey="Learned K">K Learned</name>
</author>
<author><name sortKey="Kirkup, Vm" uniqKey="Kirkup V">VM Kirkup</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="abstract" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26423047</article-id>
<article-id pub-id-type="pmc">4597324</article-id>
<article-id pub-id-type="publisher-id">1471-2105-16-S13-S10</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-16-S13-S10</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Proceedings</subject>
</subj-group>
</article-categories>
<title-group><article-title>Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Dozmorov</surname>
<given-names>Mikhail G</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>MDozmorov@vcu.edu</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Adrianto</surname>
<given-names>Indra</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Indra-Adrianto@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Giles</surname>
<given-names>Cory B</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Cory-Giles@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Glass</surname>
<given-names>Edmund</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>GlassER@vcu.edu</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Glenn</surname>
<given-names>Stuart B</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Stuart-Glenn@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Montgomery</surname>
<given-names>Courtney</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Courtney-Montgomery@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Sivils</surname>
<given-names>Kathy L</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Kathy-Sivils@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Olson</surname>
<given-names>Lorin E</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>Lorin-Olson@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A9"><name><surname>Iwayama</surname>
<given-names>Tomoaki</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>Tomoaki-Iwayama@omrf.org</email>
</contrib>
<contrib contrib-type="author" id="A10"><name><surname>Freeman</surname>
<given-names>Willard M</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<xref ref-type="aff" rid="I5">5</xref>
<email>Willard-Freeman@ouhsc.edu</email>
</contrib>
<contrib contrib-type="author" id="A11"><name><surname>Lessard</surname>
<given-names>Christopher J</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>Chris-Lessard@omrf.org</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A12"><name><surname>Wren</surname>
<given-names>Jonathan D</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I6">6</xref>
<email>Jonathan-Wren@omrf.org</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA</aff>
<aff id="I2"><label>2</label>
Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</aff>
<aff id="I3"><label>3</label>
Immunobiology and Cancer Research Program, Oklahoma Medical Research Foundation. Oklahoma City, OK, USA</aff>
<aff id="I4"><label>4</label>
Reynolds Oklahoma Center on Aging, Donald W. Reynolds Department of Geriatric Medicine, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</aff>
<aff id="I5"><label>5</label>
Department of Physiology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</aff>
<aff id="I6"><label>6</label>
Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center. Oklahoma City, OK, USA</aff>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>25</day>
<month>9</month>
<year>2015</year>
</pub-date>
<volume>16</volume>
<issue>Suppl 13</issue>
<supplement><named-content content-type="supplement-title">Proceedings of the 12th Annual MCBIOS Conference</named-content>
<named-content content-type="supplement-editor">Jonathan D Wren, Whraddah Thakkar, Ramin Jomayouni, Donald J Johann and Mikhail G Dozmorov</named-content>
<named-content content-type="supplement-sponsor">Publication of this supplement has not been supported by sponsorhsip. Information about the source of funding for publication charges can be found in the individual articles. Articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.</named-content>
</supplement>
<fpage>S10</fpage>
<lpage>S10</lpage>
<permissions><copyright-statement>Copyright © 2015 Dozmorov et al.</copyright-statement>
<copyright-year>2015</copyright-year>
<copyright-holder>Dozmorov et al.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>
) applies to the data made available in this article, unless otherwise stated.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/16/S13/S10"></self-uri>
<abstract><sec><title>Background</title>
<p>Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problematic for accurate assessment of the biological signal, yet their impact on sequencing data has not received much attention. We investigate how trimming the adapters, removing duplicates, and filtering out reads overlapping low complexity regions influence the significance of biological signal in RNA- and ChIP-seq experiments.</p>
</sec>
<sec><title>Methods</title>
<p>We assessed the effect of data processing steps on the alignment statistics and the functional enrichment analysis results of RNA- and ChIP-seq data. We compared differentially processed RNA-seq data with matching microarray data on the same patient samples to determine whether changes in pre-processing improved correlation between the two. We have developed a simple tool to remove low complexity regions, RepeatSoaker, available at <ext-link ext-link-type="uri" xlink:href="https://github.com/mdozmorov/RepeatSoaker">https://github.com/mdozmorov/RepeatSoaker</ext-link>
, and tested its effect on the alignment statistics and the results of the enrichment analyses.</p>
</sec>
<sec><title>Results</title>
<p>Both adapter trimming and duplicate removal moderately improved the strength of biological signals in RNA-seq and ChIP-seq data. Aggressive filtering of reads overlapping with low complexity regions, as defined by RepeatMasker, further improved the strength of biological signals, and the correlation between RNA-seq and microarray gene expression data.</p>
</sec>
<sec><title>Conclusions</title>
<p>Adapter trimming and duplicates removal, coupled with filtering out reads overlapping low complexity regions, is shown to increase the quality and reliability of detecting biological signals in RNA-seq and ChIP-seq data.</p>
</sec>
</abstract>
<conference><conf-date>13-14 March 2015</conf-date>
<conf-name>12th Annual MCBIOS Conference</conf-name>
<conf-loc>Little Rock, AR, USA</conf-loc>
</conference>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Oklahoma</li>
<li>Virginie</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Virginie"><name sortKey="Dozmorov, Mikhail G" sort="Dozmorov, Mikhail G" uniqKey="Dozmorov M" first="Mikhail G" last="Dozmorov">Mikhail G. Dozmorov</name>
</region>
<name sortKey="Adrianto, Indra" sort="Adrianto, Indra" uniqKey="Adrianto I" first="Indra" last="Adrianto">Indra Adrianto</name>
<name sortKey="Freeman, Willard M" sort="Freeman, Willard M" uniqKey="Freeman W" first="Willard M" last="Freeman">Willard M. Freeman</name>
<name sortKey="Freeman, Willard M" sort="Freeman, Willard M" uniqKey="Freeman W" first="Willard M" last="Freeman">Willard M. Freeman</name>
<name sortKey="Giles, Cory B" sort="Giles, Cory B" uniqKey="Giles C" first="Cory B" last="Giles">Cory B. Giles</name>
<name sortKey="Glass, Edmund" sort="Glass, Edmund" uniqKey="Glass E" first="Edmund" last="Glass">Edmund Glass</name>
<name sortKey="Glenn, Stuart B" sort="Glenn, Stuart B" uniqKey="Glenn S" first="Stuart B" last="Glenn">Stuart B. Glenn</name>
<name sortKey="Iwayama, Tomoaki" sort="Iwayama, Tomoaki" uniqKey="Iwayama T" first="Tomoaki" last="Iwayama">Tomoaki Iwayama</name>
<name sortKey="Lessard, Christopher J" sort="Lessard, Christopher J" uniqKey="Lessard C" first="Christopher J" last="Lessard">Christopher J. Lessard</name>
<name sortKey="Montgomery, Courtney" sort="Montgomery, Courtney" uniqKey="Montgomery C" first="Courtney" last="Montgomery">Courtney Montgomery</name>
<name sortKey="Olson, Lorin E" sort="Olson, Lorin E" uniqKey="Olson L" first="Lorin E" last="Olson">Lorin E. Olson</name>
<name sortKey="Sivils, Kathy L" sort="Sivils, Kathy L" uniqKey="Sivils K" first="Kathy L" last="Sivils">Kathy L. Sivils</name>
<name sortKey="Wren, Jonathan D" sort="Wren, Jonathan D" uniqKey="Wren J" first="Jonathan D" last="Wren">Jonathan D. Wren</name>
<name sortKey="Wren, Jonathan D" sort="Wren, Jonathan D" uniqKey="Wren J" first="Jonathan D" last="Wren">Jonathan D. Wren</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000115 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000115 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Pmc |étape= Checkpoint |type= RBID |clé= PMC:4597324 |texte= Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:26423047" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |