Cell filtering

[PernilleYR]

Hi SCENIC+ community :)

I am wondering if there is a motivation to perform the specific QC steps at the end of pycisTopic tutorial.
To be more specific, to perform the annotation of multiome data some filtering has already been done to keep only the high quality cells prior to SCENIC+. Is there a reason to not simply use the cells that passed that QC rather than rerunning the new QC step in SCENIC+?

I was thinking that maybe the reasoning is that the annotation is often performed on the high quality RNA cells, and this step is to keep to high quality ATAC cells.
In my project we decided to keep only cells that passed QC tresholds for both modalities. So all the cells for which I have an annotation have a good ATAC signal, but for sure I also lost some good ATAC cells (that had bad RNA). I was thinking that for consistency throughout the project it would make more sense to keep the same cells all along, but I would like to double check if there might be a reason not to do so, or if I am missing something.

Thank you for the help! :)