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). 

1. In that case, does it make sense to use `nfeature` default value `2000` while running `SelectIntegrationFeatures `.
2. 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?
3. Finally since there is no profound batch effect should I still use `SCTransform` or follow the `pbmc3K` workflow?

I am not getting many DE genes either way (with or without integration) and DE genes number fairly overlap. 

![enter image description here][1]


  [1]: /media/images/c3e82de0-d1ad-41e4-bcff-1cf6c6eb
I'd probably just try it with a few different numbers and see how it does (e.g. 2000, 1000, 500, 250, 100, etc). Hard to answer your second question without just slapping both timepoints in the same plot. I'd probably still try integration. 