Hello everyone

I am working on single cell transcriptome data (cohort A: in house data). I used seurat package for data processing which includes filtration of low quality cells, normalization (SCtransform) and clustering of the cells.

My next target is to integrate another cohort B (online published datasets) with my in-house dataset. Cohort B was normalized with Harmony Method. As there is difference in normalization in both cohort A and cohort B. I have designed following steps for the further analysis :

A) Normalize cohort A with Harmony Method B) Integrate both cohort A and cohort B with integration method (FindTransferAnchors) C) Perform clustering

Please let me know if these steps sounds right for analysis of two independent single cell datasets. I would appreciate all the suggestions.

Thanks in advance