期刊
NUCLEIC ACIDS RESEARCH
卷 45, 期 1, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkw809
关键词
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资金
- National Basic Research Program of China [2012CB316503]
- National High Technology Research and Development Program of China [2012AA020401]
- National Natural Science Foundation of China [91519326, 31361163004, 31301044]
- Tsinghua National Laboratory for Information Science and Technology Crossdiscipline Foundation
- National Institutes of Health [HG001696, 5U01HG007919-02, 5U54HG00699604, 5P50HG00773502]
- NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [R01HL122887] Funding Source: NIH RePORTER
ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for ChIA-PET data analysis, including linker trimming, read alignment, duplicate removal, peak calling and chromatin loop calling. It supports different kinds of ChIA-PET data generated from different ChIA-PET protocols and also provides quality controls for different steps of ChIA-PET analysis. In addition, ChIA-PET2 can use phased genotype data to call allele-specific chromatin interactions. We applied ChIA-PET2 to different ChIA-PET datasets, demonstrating its significantly improved performance as well as its ability to easily process ChIA-PET raw data. ChIA-PET2 is available at https://github.com/GuipengLi/ChIA-PET2.
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