software . 2019

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

Zhu, Qian; Liu, Nan; Orkin, Stuart; Yuan, Guo-Cheng;
Open Access English
  • Published: 22 Aug 2019
  • Publisher: Zenodo
Abstract
<p>We introduce CUT&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;RUN primary cleavage data. CUT&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;RUN. CUT&amp;RUNTools is available at https://bitbucket.org/qzhudfci/cutruntools/.</p>
Subjects
free text keywords: protein-DNA binding, MNase, transcription factor binding, chromatin, high-throughput sequencing, CUT&amp;RUN, CUT&amp;Tag, ATAC-seq, genomic footprinting, https://meshb.nlm.nih.gov/record/ui?name=Genomics, https://meshb.nlm.nih.gov/record/ui?name=Computational%20Biology, https://meshb.nlm.nih.gov/record/ui?name=Software, https://meshb.nlm.nih.gov/record/ui?name=Chromatin, https://meshb.nlm.nih.gov/record/ui?name=DNA-Binding%20Proteins, https://meshb.nlm.nih.gov/record/ui?name=High-Throughput%20Nucleotide%20Sequencing, https://meshb.nlm.nih.gov/record/ui?name=Transcription%20Factors, https://meshb.nlm.nih.gov/record/ui?name=DNA%20Footprinting, CUT&RUN, CUT&Tag
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Zenodo
Software . 2019
Provider: Datacite
Zenodo
Software . 2019
Provider: Datacite
Zenodo
Software . 2019
Provider: Zenodo
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software . 2019

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

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