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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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how to distinguish loop TADs and not loop TADs by using hicFindTADs #608

Closed Nuturetree closed 4 years ago

Nuturetree commented 4 years ago

Hi i statistics the length of TADs that be identified by hicFindTADs in genome， the proportion of TADs in genome always close 100%。 i guess this TADs that be identified by hicFindTADs include loop TADs and not loop TADs。i want to know how to get loop TAD by hicexplorer？

joachimwolff commented 4 years ago

Can you clarify your understanding of a loop TAD and a non-loop TAD? Unfortunately there is no clear definition of these terms and it would be helpful to help you if I know your definition of it.

Nuturetree commented 4 years ago

Can you clarify your understanding of a loop TAD and a non-loop TAD? Unfortunately there is no clear definition of these terms and it would be helpful to help you if I know your definition of it.

As we know that TAD is composed of many loops，not the entire gene region can form TAD。just like euchromatin is easier to form TAD than heterochromatin，but the analysis result by using hicFindTADs is all gene region can form TAD。i want to find loop TAD that formed by loop。so how i can do to find this TADs.

joachimwolff commented 4 years ago

If I do understand you in the correct way, we can offer hicFindTADs and hicDetectLoops, however we do not have something which can identify if a loop is a loop for its own or loop-TAD. Moreover, to identify euchromatin/hetrochromatin regions you can use hicPCA to compute the A/B compartments. I recommend to plot the results with hicPlotTADs to get the insight you like to have.

Nuturetree commented 4 years ago

OK，thanks

发自网易邮箱大师 On 10/09/2020 18:06, Joachim Wolff wrote:

If I do understand you in the correct way, we can offer hicFindTADs and hicDetectLoops, however we do not have something which can identify if a loop is a loop for its own or loop-TAD. Moreover, to identify euchromatin/hetrochromatin regions you can use hicPCA to compute the A/B compartments. I recommend to plot the results with hicPlotTADs to get the insight you like to have.

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