scRNA-seq filtering thresholds

I was given a scRNA seq dataset without any background information (e.g., mitochondrial content). I want to filter n_genes_by_counts.

Before filtering, the violin plot is heavily skewed with a heavy bottom. What cutoff threshold is appropriate?

Before filtering

enter image description here After filtering

After I remove n_genes_by_counts > 4000, the violin plot is less skewed but I'm not sure if it is overfitted. enter image description here

filtering scrna-seq

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written 4.2 years ago by melissachua90 •

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