How to interpret the output results

[wanyi0309]

Thanks for a good tool for diffrentTAD analyzaton.

When I follow the Tutorial (Example2: Testing TADs on all chromosomes), I get the result shown below：

Could I ask what does it mean when type is single, subtype is strength, and subdivide_strength_change is nan? Does it mean that this TAD has not been reorganized?

After subdividing the strength-change type into two categories, I got the *subtypes_up_down.txt file. I took out the 5th, 7th, and 8th columns of this result file and classified and counted them. The results are as follows：

For these reorganized subtypes, how can I determine which ones belong to the reorganized TADs or the TADs that differ between conditions 1 and 2?

I look forward to your answer, you will help me a lot~

[liuyc27]

Hi @wanyi0309 ,

Thank you for your question!

1. The 'python diffdomain-py3/subdivide_strength_change.py' command is used to subdivide the strength-change types into two categories. When reviewing the output file, you should first focus on the significant column. If the value of significant is 1, it indicates that the reorganized type is significant; if the value is 0, it indicates that the reorganized type is not significant. This command only subdivides significant strength-change types and writes the results into the subdivide_strength_change column. For non-significant reorganized TADs (i.e., significant=0), the subdivide_strength_change column will show as nan. Therefore, to answer your question "Could I ask what does it mean when type is single, subtype is strength, and subdivide_strength_change is nan? Does it mean that this TAD has not been reorganized?" — when the significant column is 0, as you correctly pointed out, it means that the TAD has not undergone significant reorganization.

2. strength-change, loss, split, merge, zoom, and complex are all subtypes of reorganized TADs. For detailed definitions, you can refer to this link: Example2:-Testing-TADs-on-all-chromosomes#4-demonstrations In the output file, the Type column includes the following types: loss, merge, split, and complex. The Subtype column includes zoom and strength-change. The subdivide_strength_change column further subdivides the strength-change subtype into two categories: strength-change up and strength-change down.