Urgent Question regarding topological associated domain(TAD)

[faiza-khurshid]

Hi ! XiaoTaoWang i used runHiC software. after running pileup command , i got topological associated domains(TADs) bed file . but in your pipline you did not mention that which algorithm / method you used for calling the TADs. could you please tell me which algorithm you used and which parameters or arguments will create TADs from your command line? Thank you

[XiaoTaoWang]

Which work are you referring to? In different work, we might have used different methods for TAD calling.

[faiza-khurshid]

i followed this pipeline https://xiaotaowang.github.io/HiC_pipeline/quickstart.html i firstly downloaded Hi-C dataset and reference genome data. then i ran this pileup command line $ runHiC pileup -p ../data/ -g hg38 -f HiC-SRA -F SRA -A bwa-mem -t 10 --include-readid --drop-seq --chunkSize 1500000 --logFile runHiC.log . So in resulting files i got TAD bed file like this (GSM4119020-HindIII-R1-filtered_10kb_domains.bed). but in your command line or in tutorial i could not find that which algoritm they used to create these TAD domains and boundaries bed files?

[faiza-khurshid]

Which work are you referring to? In different work, we might have used different methods for TAD calling. i followed this pipeline https://xiaotaowang.github.io/HiC_pipeline/quickstart.html i firstly downloaded Hi-C dataset and reference genome data. then i ran this pileup command line $ runHiC pileup -p ../data/ -g hg38 -f HiC-SRA -F SRA -A bwa-mem -t 10 --include-readid --drop-seq --chunkSize 1500000 --logFile runHiC.log . So in resulting files i got TAD bed file like this (GSM4119020-HindIII-R1-filtered_10kb_domains.bed). but in your command line or in tutorial i could not find that which algoritm they used to create these TAD domains and boundaries bed files?

[faiza-khurshid]

Hi ! XiaoTaoWang could you please answer my question? , because i have to present my assignment thank you

[XiaoTaoWang]

There are many methods for detecting TADs based on the .cool format. For example, you can use my another software HiTAD (https://xiaotaowang.github.io/TADLib/hitad.html) to identify TADs in a hierarchical manner.

[faiza-khurshid]

Dear XiaoTaoWang thank you for replying. your runHiC software already produced TAD bed file and TAD boundaries bed file which I described earlier. that's why iam asking how runHiC produced this TAD ?

On Thu, 29 Feb 2024, 02:17 Xiaotao Wang, @.***> wrote:

There are many methods for detecting TADs based on the .cool format. For example, you can use my another software HiTAD ( https://xiaotaowang.github.io/TADLib/hitad.html) to identify TADs in a hierarchical manner.

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[XiaoTaoWang]

For this part, I do not quite understand your question from the beginning, because runHiC does not have the module for TAD detection.