Hi-C dataBACKGROUND: 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 ...
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...
">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...
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...
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...
All raw sequencing data and the final chromosome-level haplotype-resolved genome of M.× giganteus have been deposited in the National Genomics Data Center (NGDC, https://ngdc.cncb.ac.cn) under BioProject PRJCA021366. The genome assembly of M. sativa XinJiangDaYe used as the ground truth ...
Sequencing Data Analysis Biological Data Interpretation All Informatics Education Next-generation sequencing for beginners Curious about using NGS in your research? Learn the basics of next-generation sequencing and find tips for getting started. Learn about NGS Company About Us News & Events ...
pythonbioinformaticsngshi-c3d-genomefile-formatterpairs-file UpdatedJan 31, 2025 Python YaqiangCao/cLoops Star111 Accurate and flexible loops calling tool for 3D genomic data. pythonbioinformaticsalgorithmpipelinetoolclusteringngssequencingexample-datahi-cdbscan3d-genomechia-petchromatin-interactionstripeshichip...
Sequencing Data Analysis Biological Data Interpretation All Informatics Education Next-generation sequencing for beginners Curious about using NGS in your research? Learn the basics of next-generation sequencing and find tips for getting started. Learn about NGS Company About Us News & Events ...
Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data, and chromosome conformation capture data such as Hi-C have particular challenges. Although several methods have been proposed, the most widely used type