Misleading Documentation for --tadDomains, -td Parameter in hicDifferentialTAD Tool

[GuanrongYan]

Description:
The current documentation and example provided for the hicDifferentialTAD tool might be misleading regarding the interpretation of the --tadDomains, -td parameter. According to the description, it's stated that this parameter should point to the TAD domains file computed by hicFindTADs from the treatment (experimental) dataset. However, the example provided seems to contradict this understanding by pointing to a TAD domains file (untreated_R1_domains.bed) that suggests it might be from the control (untreated) dataset instead.

Example Provided:

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$ 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
Expected Clarification:
Could the documentation be clarified to explicitly state that the --tadDomains, -td parameter should indeed refer to the TAD domains file computed from the treatment (experimental) dataset using hicFindTADs? This would ensure consistency and prevent confusion among users regarding which dataset's TAD domains file should be used in the analysis.

Thank you for considering this feedback. Please let me know if any further clarification or information is needed.