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

被引：79
|
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/.
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收藏
页数：12
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