Hello,
I have some ingle cell samples that I have merged and done QC, hashtag demultiplexing and then doublet removal. I have 2 different genotypes with big chromosomal differences so I decided to analyze all the samples together and then also separately. I was wondering when would be the correct time to subset my matrix to the different genotypes. Should I do it before normalizing and doing log on the object with all the samples or should I normalize and log after subsetting the adata object based on the genotype?
From what I understand when running sc.pp.normalize_total(adata, target_sum=1e4) it normalized per cell so both ways should yield the same results right?
Thank you
1 answer
The appropriate fork for all together vs. separated analysis is computing highly variable genes. It's the first step where cross-genotype differences could impact the results. Depending on your flavor= and subset= flags, this could be before or after normalization.
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