Skip to content

Collection of all the codes used for the paper "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells"

Notifications You must be signed in to change notification settings

Zhong-Lab-UCSD/RNA3Dgenome-code-repository

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

17 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

NCOMMS-23-21772B code repository (Zhong Lab)

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

Raw data processing

iMARGI data were processed using the publicly available iMARGI pipeline to obtain final BEDPE files used in the downstream analysis.

Data analysis and visualization

  • make_imargi_contact_matrix.r is used to create contact matrices at several resolutions from the BEDPE file.
  • MARGI_heatmap.r is used to plot contact heatmaps from contact matrices, as well as other iMARGI-related genomic tracks.
  • margi_compartment.r is used for iMARGI analysis on Hi-C A/B compartments.
  • margi_tads.r is used for iMARGI analysis on Hi-C topologically associating domains (TADs).
  • margi_loops.r is used for iMARGI analysis on Hi-C chromatin loops.

caRNA domains

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

Raw data processing

Hi-C data were processed using the publicly available 4DN Hi-C processing pipeline to obtain final .hic files used in the downstream analysis.

Data analysis and visualization

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.

About

Collection of all the codes used for the paper "Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells"

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published