How can I understand aggregate in FAN-C tool using Hi-C data?
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11 months ago
woongjaej ▴ 20

Hi, I'm a researcher from Korea using Hi-C data for some epigenetic research.

I'm using 'FAN-C aggregate' to make and calculate the interaction strength of some samples.

I have some questions about understanding it.

  1. If I have used TAD regions as input for the FAN-C aggregate, can I understand the results that they are showing the strength of each TADs?

  2. If the answer to question #1 is yes, can I say for example let's assume that the control and the other sample have the same TAD region. If the control TAD strength is 0.5 and the other sample's TAD strength is 1, can I say that the other sample's TAD strength is stronger?

  3. If the answer to question #1 is no, then how can I understand the output value for the FAN-C aggregate method?

  4. I tried to find how they are calculated, but failed. Could someone familiar with FAN-C or something like this kind of aggregating Hi-C data tell me how this aggregating is calculated?

I would appreciate help from someone who has more experience in this analysis and could clarify these questions and teach me.

Thanks a lot!

Hi-C TAD FAN-C aggregate fanc • 187 views

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