Re-clustering #9587
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Hi, Not member of the dev team. First, as fyi, I will convert this issue to discussion where it is better suited to get answers from community (as opposed to bug reports, errors, etc in Issues). The basic answer to your question is yes it is possible, but I think you need to think about why you would want to do something like this. Why use one normalization technique and then switch? If you are using SCT to help account for differences in sequencing depth these are still going to exist after subsetting so not sure why you want to switch. So what I would recommend is deeper dive into understanding the differences between the methods and your particular dataset to decide what the best course of action is for you analysis. Best, |
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Is it possible to use the SCT assay and Harmony integration for the original integrated Seurat object and then, when subclustering the individual cell types, use the RNA assay for log-normalization and Harmony?
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