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CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

Zhu, Qian; Liu, Nan; Orkin, Stuart; Yuan, Guo-Cheng


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  <identifier identifierType="DOI">10.5281/zenodo.3374112</identifier>
  <creators>
    <creator>
      <creatorName>Zhu, Qian</creatorName>
      <givenName>Qian</givenName>
      <familyName>Zhu</familyName>
      <affiliation>Dana Farber Cancer Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Liu, Nan</creatorName>
      <givenName>Nan</givenName>
      <familyName>Liu</familyName>
      <affiliation>Boston Children's Hospital</affiliation>
    </creator>
    <creator>
      <creatorName>Orkin, Stuart</creatorName>
      <givenName>Stuart</givenName>
      <familyName>Orkin</familyName>
      <affiliation>Boston Children's Hospital</affiliation>
    </creator>
    <creator>
      <creatorName>Yuan, Guo-Cheng</creatorName>
      <givenName>Guo-Cheng</givenName>
      <familyName>Yuan</familyName>
      <affiliation>Dana Farber Cancer Institute</affiliation>
    </creator>
  </creators>
  <titles>
    <title>CUT&amp;RUNTools: a flexible pipeline for CUT&amp;RUN processing and footprint analysis</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>protein-DNA binding</subject>
    <subject>MNase</subject>
    <subject>transcription factor binding</subject>
    <subject>chromatin</subject>
    <subject>high-throughput sequencing</subject>
    <subject>CUT&amp;RUN</subject>
    <subject>CUT&amp;Tag</subject>
    <subject>ATAC-seq</subject>
    <subject>genomic footprinting</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Genomics</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Computational%20Biology</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Software</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Chromatin</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=DNA-Binding%20Proteins</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=High-Throughput%20Nucleotide%20Sequencing</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=Transcription%20Factors</subject>
    <subject subjectScheme="url">https://meshb.nlm.nih.gov/record/ui?name=DNA%20Footprinting</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-08-22</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3374112</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.1101/529081</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="Cites">https://bitbucket.org/qzhudfci/cutruntools/</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3374111</relatedIdentifier>
  </relatedIdentifiers>
  <version>Initial version</version>
  <rightsList>
    <rights rightsURI="http://www.gnu.org/licenses/old-licenses/lgpl-2.0-standalone.html">GNU Library General Public License v2 or later</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;We introduce CUT&amp;amp;RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&amp;amp;RUN primary cleavage data. CUT&amp;amp;RUNTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CUT&amp;amp;RUN. CUT&amp;amp;RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.&lt;/p&gt;</description>
    <description descriptionType="Other">Please see the repository website http://bitbucket.org/qzhudfci/cutruntools/ for installation and usage information, and for updates. Usage information is also located in this software package. See README.md, INSTALL.md, and USAGE.md for details.</description>
    <description descriptionType="Other">{"references": ["Zhu et al (2019) bioRxiv 10.1101/529081v1", "Bitbucket repository site: bitbucket.org/qzhudfci/cutruntools/"]}</description>
  </descriptions>
</resource>
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