Hi, I am trying to identify clusters from my data (scRNA-seq for ~10k heart immune cells ) using Seurat4 in R server.
When I attempted to find clusters, I firstly tested resolution=0.4 in
FindClusters() and got .
( min.pct = 0.2, logfc.threshold = 0.25 for
FindAllMarkers(), I keep these parameters unchanged)
Then I used
Doheatmap() to show top20 markers, and I found obvious subclusters in several top clusters. So I increased my resolution to 0.8, 1.0, 1.5, but still it seem weird.
The figure.1~3 refer to res=0.4, 0.8, 1.5 , we can see subclusters.
SO I would like to have your advice on the causes of this situation and what to do next.
- I have used clustree to find the proper resolution, we consider 1.5 too high and unnecessary, so increasing resolution might not be a good way to solve the problem.
subsetthe cluster0 and re-run the pipeline (from
Doheatmap), the heatmap looks better, however the marker genes are different from last step. And is this a good way?
Any help or discussion will be appreciated.