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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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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Zhu, Qian</dc:creator>
  <dc:creator>Liu, Nan</dc:creator>
  <dc:creator>Orkin, Stuart</dc:creator>
  <dc:creator>Yuan, Guo-Cheng</dc:creator>
  <dc:date>2019-08-22</dc:date>
  <dc:description>We introduce CUT&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;RUN primary cleavage data. CUT&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;RUN. CUT&amp;RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.</dc:description>
  <dc:description>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.</dc:description>
  <dc:identifier>https://zenodo.org/record/3374112</dc:identifier>
  <dc:identifier>10.5281/zenodo.3374112</dc:identifier>
  <dc:identifier>oai:zenodo.org:3374112</dc:identifier>
  <dc:language>eng</dc:language>
  <dc:relation>doi:10.1101/529081</dc:relation>
  <dc:relation>url:https://bitbucket.org/qzhudfci/cutruntools/</dc:relation>
  <dc:relation>doi:10.5281/zenodo.3374111</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>http://www.gnu.org/licenses/old-licenses/lgpl-2.0-standalone.html</dc:rights>
  <dc:subject>protein-DNA binding</dc:subject>
  <dc:subject>MNase</dc:subject>
  <dc:subject>transcription factor binding</dc:subject>
  <dc:subject>chromatin</dc:subject>
  <dc:subject>high-throughput sequencing</dc:subject>
  <dc:subject>CUT&amp;RUN</dc:subject>
  <dc:subject>CUT&amp;Tag</dc:subject>
  <dc:subject>ATAC-seq</dc:subject>
  <dc:subject>genomic footprinting</dc:subject>
  <dc:subject>Genomics</dc:subject>
  <dc:subject>Computational biology</dc:subject>
  <dc:subject>Software</dc:subject>
  <dc:subject>Chromatin</dc:subject>
  <dc:subject>DNA-binding proteins</dc:subject>
  <dc:subject>High-Throughput Nucleotide Sequencing</dc:subject>
  <dc:subject>Transcription Factors</dc:subject>
  <dc:subject>DNA Footprinting</dc:subject>
  <dc:title>CUT&amp;RUNTools: a flexible pipeline for CUT&amp;RUN processing and footprint analysis</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>
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