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Script used for the study 'Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis'.

Jo, Se-Young; Kim, Eunyoung; Kim, Sangwoo


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  <identifier identifierType="DOI">10.5281/zenodo.3465870</identifier>
  <creators>
    <creator>
      <creatorName>Jo, Se-Young</creatorName>
      <givenName>Se-Young</givenName>
      <familyName>Jo</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0182-439X</nameIdentifier>
      <affiliation>Yonsei University College of Medicine</affiliation>
    </creator>
    <creator>
      <creatorName>Kim, Eunyoung</creatorName>
      <givenName>Eunyoung</givenName>
      <familyName>Kim</familyName>
      <affiliation>Yonsei University College of Medicine</affiliation>
    </creator>
    <creator>
      <creatorName>Kim, Sangwoo</creatorName>
      <givenName>Sangwoo</givenName>
      <familyName>Kim</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5356-0827</nameIdentifier>
      <affiliation>Yonsei University College of Medicine</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Script used for the study 'Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis'.</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>PDM, PDX, organoid, mouse, filtering, NGS</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-09-30</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3465870</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3465869</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Introduction&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;Scripts used for the study &amp;#39;Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analyis&amp;#39;.&amp;nbsp;ConcatRef, Disambiguate and XenofilteR are the best suggested filtering method for general purpose. Alternatively, Xenome, XenofilteR and ConcatRef are also recommended for SNV analysis. After applying filtering method, further filtering can be achieved by blacklisting using HAMA list. Estimation of contamination ratio can be used as an indicator of whether strict or lenient blacklisting should be applied.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Description&lt;/strong&gt;&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;
	&lt;p&gt;Filtering Methods&lt;/p&gt;

	&lt;ul&gt;
		&lt;li&gt;BBsplit&lt;/li&gt;
		&lt;li&gt;Bamcmp&lt;/li&gt;
		&lt;li&gt;ConcatRef&lt;/li&gt;
		&lt;li&gt;Disambiguate&lt;/li&gt;
		&lt;li&gt;TwinRef-L&lt;/li&gt;
		&lt;li&gt;TwinRef-S&lt;/li&gt;
		&lt;li&gt;XenofilteR&lt;/li&gt;
		&lt;li&gt;Xenome&lt;br&gt;
		&amp;nbsp;&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;MouseContamEstimator&lt;/p&gt;

	&lt;ul&gt;
		&lt;li&gt;Simple Python script for calculating estimated contamination level.&lt;br&gt;
		MouseContamEstimator requires &lt;a href="https://github.com/ShockYoung/BestPractice_for_PDMseq/releases/download/HAMAlist/HAMAlist.gnomad.mouse.tsv"&gt;HAMAlist&lt;/a&gt;.&lt;/li&gt;
	&lt;/ul&gt;
	&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
</resource>
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