Software Open Access

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

Zhu, Qian; Liu, Nan; Orkin, Stuart; Yuan, Guo-Cheng

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/.

Please see the repository website http://bitbucket.org/qzhudfci/cutruntools/ for installation and usage information, and for updates. Usage information is also located in this software package. See README.md, INSTALL.md, and USAGE.md for details.
Files (487.2 kB)
Name Size
cutruntools.tar.gz
md5:f2758ac7b247f827fe0c745cbeb90c54
487.2 kB Download
  • Bitbucket repository site: bitbucket.org/qzhudfci/cutruntools/

  • Zhu et al (2019) bioRxiv 10.1101/529081v1

93
15
views
downloads
All versions This version
Views 9393
Downloads 1515
Data volume 7.3 MB7.3 MB
Unique views 8787
Unique downloads 1515

Share

Cite as