Abstract 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 https://bitbucket.org/qzhudfci/cutruntools/.

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highresolution mapping identification of chromatinassociated protein binding and genomic footprinting analysis general pipeline cutrun endonuclease cut site information singlelocus binding estimates aggregate motif footprints and informative visualizations cutruntools

Qian Zhu,Nan Liu,Stuart H. Orkin,Guo-Cheng Yuan,.CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. 20 (1),.

Qian Zhu,Nan Liu,Stuart H. Orkin,Guo-Cheng Yuan,"CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis" 20

Qian Zhu,Nan Liu,Stuart H. Orkin,Guo-Cheng Yuan,"CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis"