Extract significant DEGs using Seurat FindConservedMarkers and FindAllMarkers

Question

[Jay]

Hi, When extracting significant DEGs using Seurat FindConservedMarkers or FindAllMarkers, is it correct to filter by p_val_adj < 0.05 or 0.01 and then extract them? Thanks!

[allingt]

In general, you should threshold on the p value that corresponds to the maximum FDR you can accept. In practice, for scRNA-seq data, many genes usually have a very low p value and you will probably want to define some "top" DEGs. Some people sort by p value, others filter by p value but then sort on log2FC. What will you use your extracted DEGs for?