Gained TADs in condition 2

[PinpinSui]

Hi,

Thanks for this wonderful tool to see the TAD changes among 2 condition!
How to identity the gained loops in condition 2?

Thank you,
Pinpin Sui

[Tian-Dechao]

In Condition 2, a TAD gained is equivalent to the loss of the TAD in Condition 1. To identify such TADs, swap Condition 2 as Condition 1 in the input for DiffDomain. See the example code below.
python diffdomains.py dvsd multiple <hic1> <hic0> <tadlist_of_hic1.bed>
Here, hic1 refers to the .hic file from Condition 2, while hic0 represents the .hic file from Condition 1. Additionally, tadlist_of_hic1.bed denotes the list of TADs identified in Condition 2.

[PinpinSui]

Hi Dechao,

Thank you so much for your response! So for the final list of changed TADs in condition 2, should I integrate gain to other 6 types together? I could not see the gained TAD class in Nature communication paper.

Pinpin

[Tian-Dechao]

Hey Pinpin

There is no need to integrate gained TADs into the reorganized TADs in DiffDomain. The current formulation of DiffDomain focuses on testing whether TADs from condition 1 are reorganized in condition 2, and then classifies the resulting reorganized TADs into 6 subtypes.

In cases where there are gained TADs in condition 2, we can treat condition 2 as the new condition 1 in the input of DiffDomain. This approach allows us to classify the gained TADs in condition 2 as lost TADs in condition 1, without needing to integrate them into the reorganized TADs.

Dechao

[PinpinSui]

Hi Dechao,

Appeciate your explanation! Thank you again for this wonderful diffdomain!

Pinpin

[PinpinSui]

Hi Dechao,

Thank you again! Another question, how to distinguish the strength change up and strength change down TADs with diffdomain?

Pinpin Sui