Software Open Access

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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    <subfield code="a">&lt;p&gt;We introduce CUT&amp;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;amp;RUN primary cleavage data. CUT&amp;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;amp;RUN. CUT&amp;amp;RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.&lt;/p&gt;</subfield>
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