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

[RomeroMatt]

Hi, @PinpinSui, did you ever figure out how to distinguish strength-change up/down in your conditions? I tried to do the math that was in the methods, but when I computed strength up/down, the strength in condition 2 was always in the same direction. Meaning all TADs were either up or down within a condition. I can't imagine I did the analysis correctly.

[liuyc27]

Hi @PinpinSui and @RomeroMatt,

Usage and Example 2 sections on the Wiki have been updated to introduce the methods for distinguishing between strength-change up and strength-change down TADs.For details, please refer to the following links:

• Usage
• Example 2: Testing TADs on all chromosomes

Thank you!

[RomeroMatt]

Thank you @liuyc27! I'm excited to give it a shot! -Matt