TF dropout when running runSCENIC_2_createRegulons(scenicOptions)

[rmauron]

Dear SCENIC developers,

Thanks for a great tool!

I am facing an issue when creating regulons.

I am running the SCENIC pipeline in R for 2 cell populations of interest (2 clusters out of my data set (run separately cl1 and cl2)).
Both of those cell types are expected to have a high activity of a specific TF that is well known and described.
This specific marker is upregulated in those 2 clusters.

My problem arrises in the motifs enrichment steps agains the RcisTarget databases.

In one of the cell population, my TF of interest is kept after the motifEnrichment_selfMotifs <- motifEnrichment[which(motifEnrichment$TFinDB != ""),, drop=FALSE] but in my second population, the TF is dropped out for a mysterious reason to me.
How come the same TF (highly expressed in 2 single-cell populations) could have different motifs in these populations and therefore dropped out in one?

Thanks in advance for your time!
Best