Extract significant DEGs using Seurat FindConservedMarkers and FindAllMarkers
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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?