What is the standard log2FC cut off for single cell RNA seq?

24 June 2021 1 1K Report

In bulk RNA seq we generally consider log2FC greater than 1 or less than -1 . Can I consider the same for single cell RNA seq or will it be too stringent.

Note - I am considering default value i.e 10%of the cells showing expression

Liguo Wang

Don't think there is a *standard* log2FC cutoff. YOu can use Log2FC = 0 as cutoff to call up/down-regulated genes if your experiment has a relatively small number of *significant* genes. On the other hand, if you have tens of thousands of *significant* genes, you might want to use a more stringent cutoff to narrow down the gene list to a manageable size.

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