BACKGROUND: Hi-C sequencing offers novel, cost-effective means to study the spatial conformation of chromosomes. We use data obtained from Hi-C experiments to provide new evidence for the existence of spatial gene clusters. These are sets of genes with associated functionality that exhibit close ...
This pioneering approach focused on studying the entire cell nucleus by utilizing in situ cross-linking, restriction enzyme cleavage, proximity ligation of DNA ends, and enrichment, along with high-throughput sequencing and bioinformatic analysis. Hi-C technology allowed for the exploration of DNA ...
The primary aim of qc3C is to infer the proportion of "signal" within a Hi-C sequencing library and thereby provide a means of quality control. A big advantange of qc3C is that this can be done without access to a reference sequence, which until now has been a significant stopping poin...
ChIA-PET技术( chromatin interaction analysis paired-end tag sequencing):与3C基础上发展的其他技术不同,区别在于第一步对于互作位点的 DNA 破碎不是通过限制酶进行消化,而是利用超声波击碎。然后应用抗体对特定蛋白参与的互作区段进行富集,并对这些互作区段进行消化连接,提取含有接头的双端序列( paired end tag, P...
">Downstream applications of Hi-C sequencing data). Percentage of Hi-C events Proximity ligation of chromatin in Hi-C generates interaction pairs (Hi-C events) in the form of DNA chimeras. When valid Hi-C interactions pairs (DNA chimeras) are paired-end sequenced, read 1 and read 2 will...
Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data. ...
1.HiCseg:Models the uncertainty in Hi‐C data https://cran.r-project.org/web/packages/HiCseg/index.html 2. TADbit https://github.com/3DGenomes/TADbit 3.DomainCaller http://chromosome.sdsc.edu/mouse/hi-c/download.html 4. InsulationScore:Robust to different sequencing depth; can detect dyna...
This targeted next generation sequencing technique uses biotinylated probes to capture, or enrich, regions of interest, saving time and money. Targeting specific regions of the genome focuses results, lowering the barrier to generating high-resolution Hi-C data. The Arima Capture-HiC+ platform ...
Fig. 4: Haplotyping and allele-specific analysis of RNA-seq data. a Haplotyping: Based on SNPs from Illumina sequencing larger haplotype blocks are created using PacBio long-reads. Large haplotype blocks are connected with the help of Hi-C. The breakpoints of rearrangements are also phased and...
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data genomeassemblyhi-cscaffoldingchromosomephasingsalsalachesist2thaplotypeyahs3d-dnaallhichifiasm UpdatedApr 22, 2025 Python open2c/pairtools Star112 Extract 3D contacts (.pairs) from sequencing alignments ...