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sshen82 / BandNorm

Simple Normalization Method for single-cell Hi-C
GNU General Public License v3.0
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Is depthNorm in scGAD equivalent to BandNorm? #11

Open LHXqwq opened 1 month ago

LHXqwq commented 1 month ago

Is 'depthNorm = TRUE' in the scGAD function equivalent to BandNorm? Should I first use BandNorm and then calculate the scGAD for each gene and perform 'depthNorm = TRUE', or should I directly use 'depthNorm = TRUE' in scGAD without using BandNorm?

sshen82 commented 1 month ago

Hi, The normalization in BandNorm is to eliminate the band bias among cells, and the normalization in scGAD is to eliminate the sequencing depth within gene regions for those cells. My experience is that doing BandNorm first can increase the performance, but not by a lot. If you have a huge amount of cells, you might ignore the step to save time.

Yours sincerely, Siqi Shen