variation in Boundary size after matrix correction

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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variation in Boundary size after matrix correction #686

Closed mujahida87 closed 3 years ago

mujahida87 commented 3 years ago

Hi, I also have a similar issue as my colleague raises the question below. I found that boundary sizes differ (5 to 7% of boundaries) after matrix correction (--correctionMethod ICE). I'm using the 3.6 version of hicexplorer. is it usual after matrix correction?

Thank you

joachimwolff commented 3 years ago

to what 'below' are you referring? If you refer to another issue, please specify the issue number.
what boundaries are you speaking of? TAD boundaries?

In general: Please provide more information about what you are writing about; the template to open an issue is not for fun here.

mujahida87 commented 3 years ago

Hi, I am referring to issue #679 Yes, I am talking about TAD boundaries. My bin size was 5 kb and I expect that the boundary size will be 5kb but after ICE correction, 5-7% of boundaries are larger than 5kb.

sorry for inconvenience Thank you Screenshot 2021-03-09 at 09 24 41

joachimwolff commented 3 years ago

See my comment on the other issue.

joachimwolff commented 3 years ago

Please consider my answer in https://github.com/deeptools/HiCExplorer/issues/679.