Repository of codes used for the paper "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells" (see paper).
To cite this paper: Calandrelli, R., Wen, X., Charles Richard, J. L., Luo, Z., Nguyen, T. C., Chen, C. J., ... & Zhong, S. (2023). Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nature Communications, 14(1), 6519
iMARGI data were processed using the publicly available iMARGI pipeline to obtain final BEDPE files used in the downstream analysis.
make_imargi_contact_matrix.ris used to create contact matrices at several resolutions from the BEDPE file.MARGI_heatmap.ris used to plot contact heatmaps from contact matrices, as well as other iMARGI-related genomic tracks.margi_compartment.ris used for iMARGI analysis on Hi-C A/B compartments.margi_tads.ris used for iMARGI analysis on Hi-C topologically associating domains (TADs).margi_loops.ris used for iMARGI analysis on Hi-C chromatin loops.
Data analysis: RNAStripeTools was used with default parameters to identify caRNA domains from processed iMARGI BEDPE files.
Data visualization: higlass-manage was used visualize caRNA domains.
Hi-C data were processed using the publicly available 4DN Hi-C processing pipeline to obtain final .hic files used in the downstream analysis.
Final .hic files were analyzed with the software Juicer, which was used to extract contact data as well as call A/B compartments, TADs and loops.
dump_contact_matrix.shis used to extract contact matrices at different resolutions.HiC_heatmap.ris used to plot contact heatmaps from contact matrices.compartments.shis used to call A/B compartments.compartment_analysis.ris used for analysis on A/B compartments.TADs.shis used to call TADs.TAD_analysis.ris used for analysis on topologically associating domains (TADs).loops.shis used to call loops and perform Aggregate Peak Analysis (APA).loop_analysis.ris used for analysis on chromatin loops.