Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. 3D interactions mostly occur within chromosomes (cis) rather than between chromosomes (trans), all methods detected more cis than trans interactions.
Chromatin interactions are contacts between regions far from each other on the linear DNA sequence but close in 3D space;
Function | Method | vailability | Programming language |
---|---|---|---|
Chromatin interactions | Fit-Hi-C | http://noble.gs.washington.edu/proj/fit-hi-c | Python |
Chromatin interactions | GOTHiC | http://bioconductor.org/packages/release/bioc/html/GOTHiC.html | R |
Chromatin interactions | HOMER | http://homer.ucsd.edu/homer/interactions/HiCmatrices.html | Perl, R |
Chromatin interactions | HIPPIE | http://wanglab.pcbi.upenn.edu/hippie/ | Python, Perl, R |
Chromatin interactions | diffHic | https://bioconductor.org/packages/release/bioc/html/diffHic.html | R, Python |
Chromatin interactions | HiCCUPS | https://github.com/theaidenlab/juicer/wiki/Download | Java |
TADs | HiCseg | https://cran.r-project.org/web/packages/HiCseg/index.html | R |
TADs | TADbit | https://github.com/3DGenomes/TADbit | Python |
TADs | DomainCaller | http://chromosome.sdsc.edu/mouse/hi-c/download.html | Matlab, Perl |
TADs | InsulationScore | https://github.com/dekkerlab/crane-nature-2015 | Perl |
TADs | Arrowhead | https://github.com/theaidenlab/juicer/wiki/Download | Java |
TADs | TADtree | http://compbio.cs.brown.edu/projects/tadtree/ | Python |
TADs | Armatus | https://github.com/kingsfordgroup/armatus | C++ |
【上述图表来源于: Comparison of computational methods for Hi-C data analysis 】
The total number of interactions called by each method increased with the number of reads retained by the filtering step for all tools at any resolution, although the rate of increase varied from tool to tool.
TADs are structural domains consisting of chromatin regions that are highly self-interacting but have limited interaction with regions in other domains;
TADtree: an algorithm the identification of hierarchical topological domains in Hi-C data
Arrowhead: for finding contact domains
Used bin size (resolution) of at least 40 kb for TAD calling;
cd /public/home/cotton/software/juicer/data java -jar ../CPU/juicer_tools.jar arrowhead -r 40000 -k NONE test.hic test_contact_domains_list
The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. The current method for calculating A/B compartments is based on the Principal Component Analysis (PCA) of the normalized Hi-C interaction matrix (Lieberman-Aiden et al., 2009). The first eigenvector (Principal Component 1, PC1) of the correlation matrix is then defined as the compartment score, and genomic windows with positive or negative compartment scores are defined as A or B compartment, respectively.
cd /public/home/cotton/software/juicer/data java -jar ../CPU/juicer_tools.jar eigenvector KR test.hic 1 BP 1000000 > test.Compartments
hic 文件来源于 3D DNA 流程或 java -Xmx2g -jar juicebox_tools.jar pre ;
HiCCUPS is an algorithm for finding chromatin loops.
HiCCUPS 算法包含在 juicer 软件中,可按照如下手动单独运行(有GPU节点使用):
java -Xmx2g -jar ./CPU/juicer_tools.jar hiccups -h java -Xmx2g -jar ./CPU/juicer_tools.jar hiccups /public/home/cotton/software/3d-dna/xzp/Hs1.split.hic all_hiccups_loops java -Xmx2g -jar ./CPU/juicer_tools.jar hiccups -r 40000 -p 1 -i 3 -f 0.1 -d 80000 --ignore_sparsity /public/home/cotton/software/3d-dna/xzp/Hs1.split.hic hiccups_40kb