Can't Relative Abundance take ‘estimate-unknown’ into account?

[HirokiK0]

Thank you for developing such a wonderful tool!

When comparing the relative abundance of species obtained using sylph, I would like to take into account unknown sequences.

However, the current -u option is only valid for sequence abundance and cannot be applied to relative abundance.

If there is a way to take the -u option into account for relative abundance, please let me know.

Or is it not appropriate to apply the -u option to relative abundance?

[bluenote-1577]

@HirokiK0 this is a mathematical issue. Taxonomic abundance depends in the size of the genomes. If the "unknown" genomes have small or large length, this would shift the percentage of unknown sequences.

So we don't scale taxonomic abundance by unknown content. You are free to multiply it by the percentage of unknown content, just like with sequence abundance... although this is not mathematically valid, but it's usually OK.