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I have a set of genes which were analysed with DESeq2. I expected to remove genes with low counts but I observed versus (remove genes with high coverage ). Is there any explanation for this reason?
Outliers are removed, on both sides. Are those genes highly expressed in all samples or just a few?
If removed genes have high counts in all samples what is your explanation? @WouterDeCoster
How high is "high coverage"? DESeq2 performs a few different kinds of filtering. At the gene level, though, it only filters for maximal power. Regardless of how high the counts are, presumably that's why the gene got filtered. You can disable that (look for "independent filtering" in the documentation) if it's a problem.