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

被引：76

作者：

Zhu, Qian ^{[1
,2
]}

Liu, Nan ^{[3
,4
]}

Orkin, Stuart H. ^{[3
,4
,5
]}

Yuan, Guo-Cheng ^{[1
,2
]}

机构：

[1] Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA

[2] Harvard Chan Sch Publ Hlth, Boston, MA 02115 USA

[3] Dana Farber Canc Inst, Canc & Blood Disorders Ctr, Boston, MA 02115 USA

[4] Harvard Med Sch, Boston Childrens Hosp, Boston, MA 02115 USA

[5] Howard Hughes Med Inst, Boston, MA 02115 USA

来源：

GENOME BIOLOGY | 2019年 / 20卷 / 01期

关键词：

TRANSCRIPTION; CHROMATIN; IDENTIFICATION; ELEMENTS; BINDING; GENE; LMO2; BIAS;

D O I：

10.1186/s13059-019-1802-4

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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/.

引用

页数：12

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