.hic to .cool

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Nov 23, 2024, 10:10:42 PM11/23/24

to 3D Genomics

Is there a tested way to convert hic files created through Juicer to cool files? I tried using hic2cool but got unicode error. Although not hic2cool, found more or less the same error here at this issue - https://github.com/deeptools/HiCExplorer/issues/798#issuecomment-1142319166

Are there any other tools or workaround to get this conversion done? Am I missing something? Please let me know :‑)

Regards,

Aman

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Nov 25, 2024, 5:30:50 PM11/25/24

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Hi, Aman
I'm not 100% sure it will help, but you may try using hictk (https://hictk.readthedocs.io/en/stable/format_conversion.html)

Nikita

воскресенье, 24 ноября 2024 г. в 04:10:42 UTC+1, amen...@gmail.com:

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May 11, 2025, 8:00:24 PMMay 11

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Hi Aman,

It might be too late, but in case: to convert .hic files to .cool, I used the `hicConvertFormat` function from HiCExplorer as such:

hicConvertFormat -m matrix.hic \
--inputFormat hic \
--outputFormat cool \
-o matrix.cool \

--resolutions

I don't know how this issue that you cited arose, but I had no issue, so it might have been fixed.

Hope this can help,

Best wishes,

Alice

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