Published August 22, 2019 | Version Initial version
Software Open

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

Creators

  • 1. Dana Farber Cancer Institute
  • 2. Boston Children's Hospital

Description

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/.

Notes

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.

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Additional details

Related works

Cites
10.1101/529081 (DOI)
https://bitbucket.org/qzhudfci/cutruntools/ (URL)

References

Subjects

Genomics
https://meshb.nlm.nih.gov/record/ui?name=Genomics
Computational biology
https://meshb.nlm.nih.gov/record/ui?name=Computational%20Biology
Software
https://meshb.nlm.nih.gov/record/ui?name=Software
Chromatin
https://meshb.nlm.nih.gov/record/ui?name=Chromatin
DNA-binding proteins
https://meshb.nlm.nih.gov/record/ui?name=DNA-Binding%20Proteins
High-Throughput Nucleotide Sequencing
https://meshb.nlm.nih.gov/record/ui?name=High-Throughput%20Nucleotide%20Sequencing
Transcription Factors
https://meshb.nlm.nih.gov/record/ui?name=Transcription%20Factors
DNA Footprinting
https://meshb.nlm.nih.gov/record/ui?name=DNA%20Footprinting