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

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/ .

SUBMITTER: Zhu Q 

PROVIDER: S-EPMC6734249 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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

Zhu Qian Q   Liu Nan N   Orkin Stuart H SH   Yuan Guo-Cheng GC  

Genome biology 20190909 1

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 a  ...[more]

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