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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Is the input data distance-normalized count or raw count? #105

Closed sotuamax closed 3 weeks ago

sotuamax commented 3 weeks ago

Hi,

I have some questions about the input data. I have both cool and hic format, and I can transform them to the required format for dchic. However, after reading the paper, it is clear that distance-normalized count is required for SVD decomposition. Should I provide distance-normalized matrix count as input? Or raw count data is also okay as the program can do the distance-normalization on the data.

In addition, would any matrix normalization, like KR, ICE, recommended on the matrix count?

Many thanks for your clarification.

Best,

ay-lab commented 3 weeks ago

Hi,

Please provide the raw count matrix as input. dcHiC will perform the distance normalization. We don't recommend any normalization. Thanks.

sotuamax commented 3 weeks ago

Thank you!

Best,