Hi everyone. I am dealing with a parasite that contains
~5000 genes. The scRNAseq data is from a stage of its life cycle where few genes are expressed (the median genes expressed are ~100 in our data).
- In that case, does it make sense to use
- Also, the UMAP looks as given below (we have data from two-time points with 1 hr difference between T1 and T2). So should I perform integration or not?
- Finally since there is no profound batch effect should I still use
SCTransformor follow the
I am not getting many DE genes either way (with or without integration) and DE genes number fairly overlap.