What to deal with biological replicates?
Hi 10x friends,
In my recent single-cell gene expression experiment, I have one control and two disease samples with close (+/- 10-15% ) cells and some variation of mean reads/cell in these samples.
For the two disease samples, should I merge them then compared to the control? Or, should I compare them one by one to the control - but then I may have two slightly different conlusion?
Re: What to deal with biological replicates?
I would suggest using our cellranger aggr pipeline to combine all three samples. By default the aggr pipeline will subsample reads from higher-depth GEM wells until they all have an equal number of confidently mapped reads per cell.
You can find more detailed documentation here: