we applied it to enhance the Hi-C dataset from aorta tissue where only low-resolution (40 kb) matrices are available (Fig.5d). By comparing chromatin interactions from Capture Hi-C, we observe that HiCPlus-enhanced matrix captures significant interactions betweenMYCpromoter andcis-regulatory ele...
Results: We have developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a Hi-C dataset, performs high-resolution MDS separately on each partition, and then reassembles the partitions using low-resolution MDS. miniMDS is faster, more accurate, and uses less memory ...
How to determine the proper binsize for a given Hi-C remains an open question. Intuitively, the best binsize should be the one that reliably captures the most essential structure of a given Hi-C dataset. Because SE characterizes the uncertainty of the high-dimensional hierarchical structure of ...
Setup a new test folder and download a small Hi-C dataset mapped to sacCer3 genome: $ mkdir /tmp/test-pairtools $cd/tmp/test-pairtools $ wget https://github.com/mirnylab/distiller-test-data/raw/master/bam/MATalpha_R1.bam Additionally, we will need a .chromsizes file, a TAB-separate...
However, the distribution of cut sites in these cases is not uniform, and there are always some genomic regions that are not well represented in a Hi-C dataset prepared using restriction enzymes. Second, nucleases that have no sequence-specific cutting preferences, such as DNase I [21,22,23...
0笔记 共2个版本 开学季特惠,9月3日-11月30日,专业版用户每周AI豆3倍膨胀,快来领取吧! 摘要原文 Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analy...
To see the the results of a test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation. Credits nf-core/hic was originally written by Nicolas Servant. Contr...
wherenexpis the total number of interactions classified as significantly differential for a particular looping class using the experimental conditionsTandnnullis the total number of interactions classified as significantly differential in the null dataset, which approximates FPRexp. ...
c The first eigenvector of the HiC-IMR90-2014 Hi-C dataset. d The smoothed first eigenvector of the binned correlation matrix of the 450 k-fibroblast dataset. e The difference between (a) and (c). f the difference between (b) and (d). The high correlation between (e) and (f) ...
吕红强,博士,副教授,研究方向:生物大数据分析与处理。E-mail:hongqianglv@mail.xjtu.edu.cn。 摘要 染色体的空间交互作用被视为影响基因表达调控的重要因素,高通量染色体构象捕获(high-throughput chromosome conformation capture, Hi-C)技术已成为3D基因组学中探索染色体空间交互作用的主要实验手段之一。随着Hi-C样本数...