Comments (2)
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I'm transitioning from RNA-Seq analysis, where I would leave DESeq2 use it's built-in expression filters to remove lowly-expressed genes, so I'm having some trouble to establish the prevalence filter thresholds. Currently, I'm considering a given ASV present if it's abundance is at least 0.01% of the total sample reads (I'm using relative abundances because my samples have a highly variable number of reads). Then, I filter out ASVs that are present in less than 5% of the samples.
The downstream analysis I'm planning to do are PERMANOVA (to check whether samples differ between groups), DESeq2+ZINBWAVE differential abundance tests and discovering the "core" ASVs of each group.
Thank you for the resources!
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Related Issues (20)
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