DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis
DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis
Abstract BackgroundIt is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) is a new technology with high efficiency and effective cost for whole-genome chromosome conformation capture. ResultsHere, we introduce DLO Hi-C Tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied DLO Hi-C Tool to different DLO Hi-C datasets, and demonstrated its ability of processing large data in multi-threading. ConclusionsDLO Hi-C Tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.
Li Guoliang、Hong Ping、Cao Gang、Jiang Hao、Lin Da、Xu Weize、Xu Qian
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University||Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University||Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University||Bio-Medical Center, Huazhong Agricultural University||College of Veterinary Medicine, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University||Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University||Bio-Medical Center, Huazhong Agricultural University||College of Veterinary Medicine, Huazhong Agricultural UniversityState Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University||Bio-Medical Center, Huazhong Agricultural University||College of Veterinary Medicine, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University||Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University
生物科学研究方法、生物科学研究技术分子生物学生物工程学
3D genomicsDLO Hi-CPipeline
Li Guoliang,Hong Ping,Cao Gang,Jiang Hao,Lin Da,Xu Weize,Xu Qian.DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis[EB/OL].(2025-03-28)[2025-07-16].https://www.biorxiv.org/content/10.1101/764332.点此复制
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