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

Genome Biol. 2019 Sep 9;20(1):192. doi: 10.1186/s13059-019-1802-4.


We introduce CUT&RUNTools as a flexible, general pipeline for facilitating the identification of chromatin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN primary cleavage data. CUT&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&RUN. CUT&RUNTools is available at .

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / metabolism
  • Endonucleases
  • GATA1 Transcription Factor / analysis
  • Humans
  • Protein Footprinting / methods*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Software*
  • Stem Cells / metabolism


  • Chromatin
  • GATA1 Transcription Factor
  • GATA1 protein, human
  • Endonucleases