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XiaoTaoWang / domaincaller

A Python implementation of the original DI domain caller
GNU General Public License v3.0
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cannot detect the TAD boundary location #2

Open caragraduate opened 1 year ago

caragraduate commented 1 year ago

Hi there,

Thank you for your contribution to the Python version of the DI TAD calling algorithm, which is more convenient to use. I have one question regarding the output files of .DIs.bedGraph and .tad.bed. I actually see all the detected TADs are consecutive from the .tad.bed file, which means there is no boundary break between two adjacent TADs. Is this the correct output to expect and is this how the DI work actually? Or it implies I am missing sth during the processing?

Looking forward to your reply, and thx a lot!

A sample output in the .tad.bed file looks like this: chr1 820000 895000 chr1 895000 920000 chr1 920000 1040000 chr1 1040000 1120000 chr1 1120000 1160000 chr1 1160000 1200000 chr1 1200000 1235000 chr1 1235000 1280000 chr1 1280000 1330000 chr1 1330000 1420000 ......

Naveen-Ahuja commented 1 year ago

Hi,

I was just wondering how you got domaincaller to work. After creating the environment and running it I keep getting this error,

ImportError: cannot import name '_MAX_WINDOWS_WORKERS' from 'concurrent.futures.process' (/Users/naveen/opt/anaconda3/envs/domaincaller/lib/python3.7/concurrent/futures/process.py)

thank you

Tomos-cell commented 1 year ago

Hi,

I was just wondering how you got domaincaller to work. After creating the environment and running it I keep getting this error,

ImportError: cannot import name '_MAX_WINDOWS_WORKERS' from 'concurrent.futures.process' (/Users/naveen/opt/anaconda3/envs/domaincaller/lib/python3.7/concurrent/futures/process.py)

thank you

I met the same problem and I adjusted python version from 3.7.1 to 3.7.10. Maybe you can try.

Naveen-Ahuja commented 1 year ago

Thank you, that worked.

Were any of your TADs miss aligned with your hic contact map? eg

Screen Shot