How to ID cell types using reference scRNAseq dataset


I'm very new to scRNAseq analysis, and I really appreciate any inputs and comments. Your feedback would help me a lot.

I have been given 3 groups data (4 normal, 8 disease and 8 treatment samples), what is the workflow to identify how man cell types and also ID the cell types using reference dataset( in each group?

This question might sounds too general. Specifically, I wonder whether I need to merge data within each group and then perform analysis for each group separately? or I should merge and integrate all 20 samples together? For QC, from my limited understanding, I should perform QC on each samples (20 in total) before doing any computation analysis, right?

Thank you so much for the kindly help!





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