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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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  "description": "<p>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/.</p>", 
  "license": "http://www.gnu.org/licenses/old-licenses/lgpl-2.0-standalone.html", 
  "creator": [
    {
      "affiliation": "Dana Farber Cancer Institute", 
      "@type": "Person", 
      "name": "Zhu, Qian"
    }, 
    {
      "affiliation": "Boston Children's Hospital", 
      "@type": "Person", 
      "name": "Liu, Nan"
    }, 
    {
      "affiliation": "Boston Children's Hospital", 
      "@type": "Person", 
      "name": "Orkin, Stuart"
    }, 
    {
      "affiliation": "Dana Farber Cancer Institute", 
      "@type": "Person", 
      "name": "Yuan, Guo-Cheng"
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  "url": "https://zenodo.org/record/3374112", 
  "citation": [
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  "datePublished": "2019-08-22", 
  "version": "Initial version", 
  "keywords": [
    "protein-DNA binding", 
    "MNase", 
    "transcription factor binding", 
    "chromatin", 
    "high-throughput sequencing", 
    "CUT&RUN", 
    "CUT&Tag", 
    "ATAC-seq", 
    "genomic footprinting"
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  "identifier": "https://doi.org/10.5281/zenodo.3374112", 
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  "name": "CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis"
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