I used Signac package for analyzing Single cell ATAC-Seq based on main tutorial, see following:
Basically, I have worked on a 10x sample with ~4000 cells (scATAC-SEQ). I have faced with a problem. I have tried different resolution but I can't see any significant peaks in FindMarkers function for number of clusters in Signac package. ( I have tried both FindMarker and FindAllMarker but results in 0 peaks).
For example in res. 0.3 = the first biggest cluster has no significant peak in the output, also in res. 0.8 from 14 clusters 4 of them has no significant peaks output,
However, in RNA level I could found markers in all resolutions.
What is the problem with this analysis ? How can I fix it?