aertslab
using scenicplus
Where is the defualt human scATAC-seq human data file I can use for scenicplus? Is there a defualt file for mouse?
I want to be able to run grnboost, RCisTarget, and AUcell analaysis by providing gene expression matrix as input.
What are the basic commands I need to perform?
Hi @crossworlds423
Can you specify what you mean by the default scATAC-seq human data file?
In order to be able to run SCENIC+ you will need your own scATAC-seq data that is paired with the scRNA-seq data you are analysing. Either through a multiome experiment or through performing seperate scATAC-seq and scRNA-seq on very similar samples.
Best, Seppe
Is it ok if we use any kinda of scATAC-seq data that matches the type of tissue associated with the scRNA-seq data we are analysing?
Normally this wouldn't make sense but we do not have any scATAC-seq data to work with. We currently only have scRNA-seq data.
Hi @crossworlds423
You can use scATAC-seq that kind of matches but you need to be able to match clusters from the scATAC-seq with clusters from the scRNA-seq in order to be able to run SCENIC+ (also you will only be able to run it for the clusters that match, not for the others).
Best,
Seppe
@SeppeDeWinter I have a similar question. We currently only have scRNA-seq data too, and we don't need scATAC-seq data in our research now. Could we perform the same analysis that scenic does using scenic+ ? Though we can persue our research using scenic, we want to switch to scenic+, then we can be familiar with scenic+ and use scenic+ if we have scATAC-seq data later.
