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