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

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.

{"references": ["Zhu et al (2019) bioRxiv 10.1101/529081v1", "Bitbucket repository site: bitbucket.org/qzhudfci/cutruntools/"]}

Related Organizations

Dana-Farber Cancer Institute
United States
Boston Children's Hospital
United States

Keywords

https://meshb.nlm.nih.gov/record/ui?name=DNA%20Footprinting, CUT&Tag, https://meshb.nlm.nih.gov/record/ui?name=DNA-Binding%20Proteins, https://meshb.nlm.nih.gov/record/ui?name=Computational%20Biology, high-throughput sequencing, https://meshb.nlm.nih.gov/record/ui?name=Genomics, protein-DNA binding, ATAC-seq, genomic footprinting, CUT&RUN, CUT&RUN, transcription factor binding, https://meshb.nlm.nih.gov/record/ui?name=Software, chromatin, MNase, CUT&Tag, https://meshb.nlm.nih.gov/record/ui?name=Transcription%20Factors, https://meshb.nlm.nih.gov/record/ui?name=Chromatin, https://meshb.nlm.nih.gov/record/ui?name=High-Throughput%20Nucleotide%20Sequencing

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