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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicInterIntraTAD : output value for strongest TAD (which is related with highly expressed genes) in the sample? #804

Open JungWoongJae opened 2 years ago

JungWoongJae commented 2 years ago

Hi, I'm recently using HiCExplorer to analyze my Hi-C data.

First, thank you for the fantastic tool for researchers to use! :)

I have a question using the hicInterIntraTAD tool in HiCExplorer.

I have defined TAD regions on my own and used its bed file for input data in hicInterIntraTAD, and then the tool gave me output files with various values.

I'm trying to find out the strongest TAD in the sample. In previous studies on TAD strength, it seemed they call it domain score. (ex. More expressed genes involving TAD has greater domain score, and weakly expressed genes involving TAD has lower domain score)

Is there a value that I can use as a domain score equally or at least as similar?

I tried to look into the values matching with other data, but it was uncertain for me to do it alone..

I will be very grateful if you could give me some advice.

Thanks a lot!