pyscenic feather file

Question

[Andy]

I am running my PySCENIC analysis and have a question. For the feather file, do you use the gene-based or region-based approach? I know that the gene-based approach can be useful for identifying TFs that are highly active across multiple cell types and for identifying target genes of those TFs. The region-based approach can be useful for identifying TFs that are highly active in specific genomic regions. I am wondering if it is necessary to conduct both gene-based and region-based analyses for your dataset.