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Exploring Contact Distance Distributions with Google Colaboratory.

Ryuichiro Nakato
Published in: Methods in molecular biology (Clifton, N.J.) (2024)
Hi-C and Micro-C are the three-dimensional (3D) genome assays that use high-throughput sequencing. In the analysis, the sequenced paired-end reads are mapped to a reference genome to generate a two-dimensional contact matrix for identifying topologically associating domains (TADs), chromatin loops, and chromosomal compartments. On the other hand, the distance distribution of the paired-end mapped reads also provides insight into the 3D genome structure by highlighting global contact frequency patterns at distances indicative of loops, TADs, and compartments. This chapter presents a basic workflow for visualizing and analyzing contact distance distributions from Hi-C data. The workflow can be run on Google Colaboratory, which provides a ready-to-use Python environment accessible through a web browser. The notebook that demonstrates the workflow is available in the GitHub repository at https://github.com/rnakato/Springer_contact_distance_plot.
Keyphrases
  • electronic health record
  • genome wide
  • high throughput sequencing
  • gene expression
  • dna damage
  • high throughput
  • dna methylation
  • oxidative stress
  • artificial intelligence