How to use HiCExplorer for TAD analysis with HiCPro input

[PanZiwei]

Hi, I want to do downstream TAD analysis with HiCExplorer. I have already used HiCPro to get the matrix (both iced and raw) already. I am wondering whether it is possible to ask you several questions:

1. How do you decide the resolution when calling TAD and compare the differential TAD?

2. For hicDifferentialTAD example uasge: hicDifferentialTAD -tm GSM2644945_Untreated-R1.100000_chr1.cool -cm GSM2644947_Auxin2days-R1.100000_chr1.cool -td untreated_R1_domains.bed -o differential -p 0.01 -t 4 -mr all

   a. Are the paired inputs with a specific resolution such as 40kb to call TAD?

   b. Where should I get the .cool file after HiCPro?
   Here is what I did right now: Use hic pro to process the fastq with 40kb resolution -> HiCpro result raw contact matrix(WT1_40000.matrix) -> Convert raw contact matrix to .cool format. Should I use raw matrix or iced matrix? Can I use the converted .cool result as the input for hicDifferentialTAD?

   c. What if the -tm and -cm have biological replicates? Are you calculating the average before finding the diffferential TAD?

   d. For -td, how can I get the bed file? Should I used the untreated_abs.bed produced by HiCPro as suggested in https://github.com/deeptools/HiCExplorer/issues/752#issuecomment-917996876?

3. Does hicFindTADs accept .cool format as input? If so, what is the example usage? In the example usage it only shows the .h5.

4. What is the difference between the function hicDifferentialTAD and hicFindTADs?

Thanks!