30 May 2025 0 7K Report

I have recently applied TopDom to my 40kb-resolution Hi-C data and have obtained some intriguing results. However, I have encountered some confusion regarding the output files, particularly the meaning of the "tag" column in the .domain and .bed files.

  • Continuous Regions Tagged as 'domain': In the output files, I have noticed many continuous regions that are tagged as 'domain'. I am curious to know if these regions represent 'TAD domains'. Could you please clarify the meaning of these tags and confirm if they indeed correspond to TAD domains?
  • Interpreting 'TAD Boundaries': I understand that 'TAD boundaries' should represent the edges of TAD domains. However, I have observed that the number of regions tagged as 'boundary' is relatively low. This leads me to wonder which of the following interpretations is correct: The edges of regions tagged as 'domain' represent TAD boundaries. The regions explicitly tagged as 'boundary' represent TAD boundaries. Could you please provide guidance on which interpretation is accurate?
  • Continuous Regions Tagged as 'boundary': I have also noticed that there are continuous regions tagged as 'boundary'. Given that TAD domains are typically separated by single boundaries, I am puzzled by the presence of multiple continuous boundary regions. Could you explain why this might be the case and how these continuous boundary regions should be interpreted?

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