High depth genome wide chromatin contact matrix

These high-depth meta-Hi-C chromatin contact matrices are surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, eQTLs, and cross-species relationships. 
For building the meta-Hi-C matrix, we uniformly processed 3619, 6732, and 487 Hi-C runs for Human, Mouse, and Fly respectively. The runs were obtained after querying Sequence Read Archive with field limitations of given species and Hi-C as experiment strategy.  A genome-wide chromatin contact matrix was created for each run after mapping the reads to the same reference genome for each species. Reads were aligned to the hg38, mm10, and dm6 genomes in Human, Mouse and Fly respectively. All chromatin contact matrices for a species were aggregated to create the meta-Hi-C matrix. 
The genome-wide Hi-C matrices were divided into cis (intrachromsomal) and trans (interchromosomal). In cis, each chromosome is stored in a seperate matrix. In trans,  the matrix is genome-wide but with no cis contacts (cis contacts are always 0 in this case). Here the cis contact matrices are available at 10KB and 1KB resolution for all three species. The trans contact matrices are available at 10KB resolution for all three species and additionally at 1KB resolution for Fly. The matrices are stored as *.h5 in HiCMatrix format (https://github.com/deeptools/HiCMatrix). HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/) can be used to process these files or to convert them to other formats if desired. 
Meta-Hi-C matrices at several other resolutions are available for download via online tool at https://gillisweb.cshl.edu/HiC/ or direct download at https://labshare.cshl.edu/shares/gillislab/resource/HiC/

这些深度极高的元Hi-C染色质互作矩阵在捕捉染色质互作的长距离功能关系方面出人意料地强大，如今它们能够预测共表达、eQTLs以及跨物种关系。构建元Hi-C矩阵时，我们对人类、小鼠和果蝇分别进行了3619、6732和487次Hi-C实验的处理。这些实验是在对序列读取档案进行查询时，通过限制给定物种和Hi-C实验策略来获取的。在将读取序列映射到每个物种的相同参考基因组后，为每个物种创建了全基因组染色质互作矩阵。在人类、小鼠和果蝇中，分别对hg38、mm10和dm6基因组进行了读取对齐。将一个物种的所有染色质互作矩阵汇总，以创建元Hi-C矩阵。
全基因组Hi-C矩阵被分为顺式（同源染色体）和反式（异源染色体）。在顺式中，每个染色体存储在一个单独的矩阵中。在反式中，矩阵是全基因组的，但没有顺式接触（在这种情况下，顺式接触始终为0）。在此，顺式接触矩阵以10KB和1KB分辨率提供所有三个物种的数据。反式接触矩阵以10KB分辨率提供所有三个物种的数据，并为果蝇提供1KB分辨率的数据。这些矩阵以*.h5格式存储为HiCMatrix格式（https://github.com/deeptools/HiCMatrix）。可以使用HiCExplorer（https://hicexplorer.readthedocs.io/en/latest/）处理这些文件或将它们转换为其他格式。
可通过在线工具https://gillisweb.cshl.edu/HiC/或直接下载https://labshare.cshl.edu/shares/gillislab/resource/HiC/获取不同分辨率的元Hi-C矩阵。