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Title:          Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Subject:        BMC Genomics, 2015, doi:10.1186/s12864-015-1975-5
Keywords:       Transposons,Mobile elements,NGS,Somatic mutation,Cancer,Structural variation,Genomics,Evolution
Author:         Elizabeth Hénaff
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        Title: Results
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      Title: Background
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      Title: Results and discussion
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        Title: An algorithm for identification of transposon insertion sites using paired-end and clipped reads
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        Title: Identification of homozygous TEIs in Arabidopsis using real reads and a simulated reference
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        Title: Identification of heterozygous TEIs in human genomes using simulated reads
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        Title: Distinguishing somatic and germline TEIs using simulated matched tumor-normal pairs
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        Title: TEI filter optimization
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        Title: Identification of somatic TEIs
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        Title: Primer design to verify insertions and sequence inserted element
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        Title: Simulation of TEIs in the Arabidopsis thaliana Col-0 reference genome
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        Title: Simulation of TEIs and Illumina reads for the human reference hg19
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        Title: Analysis of simulated tumor-normal pairs
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        Title: Detection of TEIs in the Arabidopsis thaliana Ler-1 strain
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        Title: Validation of Ler-1 TEIs using long reads from PacBio-SMRT
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        Title: Detection and validation of TEIs in a human 1000GP trio
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        Title: Running RetroSeq
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        Title: Data and software availability
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    Author: Elizabeth Hénaff
    Subject: BMC Genomics, 2015, doi:10.1186/s12864-015-1975-5
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         <prism:publicationName>BMC Genomics</prism:publicationName>
         <prism:copyright>Hénaff et al.</prism:copyright>
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               <rdf:li>Mobile elements</rdf:li>
               <rdf:li>NGS</rdf:li>
               <rdf:li>Somatic mutation</rdf:li>
               <rdf:li>Cancer</rdf:li>
               <rdf:li>Structural variation</rdf:li>
               <rdf:li>Genomics</rdf:li>
               <rdf:li>Evolution</rdf:li>
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         <dc:title>
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               <rdf:li xml:lang="x-default">Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution</rdf:li>
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               <rdf:li>Luís Zapata</rdf:li>
               <rdf:li>Josep M. Casacuberta</rdf:li>
               <rdf:li>Stephan Ossowski</rdf:li>
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                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
                        </rdf:li>
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                  <pdfaSchema:schema>crossmark</pdfaSchema:schema>
                  <pdfaSchema:property>
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                           <pdfaProperty:name>CrossMarkDomains</pdfaProperty:name>
                           <pdfaProperty:valueType>Seq Text</pdfaProperty:valueType>
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                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:description>Usual same as prism:doi</pdfaProperty:description>
                           <pdfaProperty:name>DOI</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                  <pdfaSchema:schema>Prism</pdfaSchema:schema>
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                        <rdf:li rdf:parseType="Resource">
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                           <pdfaProperty:description>The aggregation type specifies the unit of aggregation for a content collection. 
Comment 
PRISM recommends that the PRISM Aggregation Type Controlled Vocabulary be used to provide values for this element. 
Note: PRISM recommends against the use of the #other value currently allowed in this controlled vocabulary. In lieu of using #other please reach out to the PRISM group at info@prismstandard.org to request addition of your term to the Aggregation Type Controlled Vocabulary. 

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                           <pdfaProperty:name>aggregationType</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Copyrigh</pdfaProperty:description>
                           <pdfaProperty:name>copyright</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>The Digital Object Identifier for the article.
The DOI may also be used as the dc:identifier. If used as a dc:identifier, the URI form should be captured, and the bare identifier should also be captured using prism:doi. If an alternate unique identifier is used as the required dc:identifier, then the DOI should be specified as a bare identifier within prism:doi only. 
If the URL associated with a DOI is to be specified, then prism:url may be used in conjunction with prism:doi in order to provide the service endpoint (i.e. the URL). 
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                           <pdfaProperty:name>doi</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>ISSN for an electronic version of the issue in which the resource occurs. 
Permits publishers to include a second ISSN, identifying an electronic version of the issue in which the resource occurs (therefore e(lectronic)Issn. If used, prism:eIssn MUST contain the ISSN of the electronic version. See prism:issn. 
</pdfaProperty:description>
                           <pdfaProperty:name>issn</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>Title of the magazine, or other publication, in which a resource was/will be published. 
Typically this will be used to provide the name of the magazine an article appeared in as metadata for the article, along with information such as the article title, the publisher, volume, number, and cover date. 

Note: Publication name can be used to differentiate between a print magazine and the online version if the names are different such as “magazine” and “magazine.com.” 
</pdfaProperty:description>
                           <pdfaProperty:name>publicationName</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
                        </rdf:li>
                        <rdf:li rdf:parseType="Resource">
                           <pdfaProperty:category>external</pdfaProperty:category>
                           <pdfaProperty:description>This element provides the url for an article or unit of content. 
The attribute platform is optionally allowed for situations in which multiple URLs must be specified. PRISM recommends that a subset of the PCV platform values, namely “mobile” and “web”, be used in conjunction with this element. 
NOTE: PRISM recommends against the use of the #other value allowed in the PRISM Platform controlled vocabulary. In lieu of using #other please reach out to the PRISM group at prism-wg@yahoogroups.com to request addition of your term to the Platform Controlled Vocabulary. 
</pdfaProperty:description>
                           <pdfaProperty:name>url</pdfaProperty:name>
                           <pdfaProperty:valueType>Text</pdfaProperty:valueType>
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