Detecting TAD-like domains from RNA-associated interactions

The example data comprises six files. One is the RNA-chromatin contact map of chr22 constructed from iMARGI HEK dataset (iMARGI_chr22_RAI_matrix_100kb.txt). For Hi-C data, we collect the contact map of chr22 from the Hi-C HEK293T dataset (HEK293T_chr22_100KR_matrix.txt) as well as the detected TADs result (HEK293T_chr22_100KR_matrix.txt.multi2D_AllH2_sparse.tsv). To evaluate the epigenetic characteristic enrichment of inferred TAD-like domains, we download the CTCF TF ChIP-seq peaks (CTCF_ENCFF206AQV.bed), the result of fold change over control of H3K27me3 (H3K27me3_hg38_GSM3907592.bedgraph) and H3K36me3 (H3K36me3_hg38_ENCSR910LIE.bedgraph). The software SuperTLD (https://github.com/deepomicslab/SuperTLD) can directly take the data as input. Usage: uncompress the example_data.zip into the directory of ./data本示例数据集包含六个文件。其一为基于iMARGI HEK数据集构建的22号染色体RNA-染色质接触图谱（iMARGI_chr22_RAI_matrix_100kb.txt）。针对Hi-C数据，我们从HEK293T数据集获取了22号染色体的接触图谱（HEK293T_chr22_100KR_matrix.txt），以及经检测得到的拓扑关联结构域（Topologically Associating Domain，简称TAD）结果文件（HEK293T_chr22_100KR_matrix.txt.multi2D_AllH2_sparse.tsv）。为评估所推断的类TAD结构域的表观特征富集程度，我们下载了CTCF转录因子的染色质免疫沉淀测序（Chromatin Immunoprecipitation Sequencing，简称ChIP-seq）峰文件（CTCF_ENCFF206AQV.bed）、H3K27me3相较于对照组的折叠变化结果文件（H3K27me3_hg38_GSM3907592.bedgraph），以及H3K36me3的对应结果文件（H3K36me3_hg38_ENCSR910LIE.bedgraph）。软件SuperTLD（https://github.com/deepomicslab/SuperTLD）可直接将本数据集作为输入。使用方法：将example_data.zip解压至./data目录下。