How to determine the relative abundance

Question

[serene.s]

Hi everyone! I have a very silly question, I have used a tool called eukdetect to detect the eukaryotic species present in my metagenomic samples. So they have given the results for the individual samples in two formats as mentioned below in the files. So, now I want to do compare and plot different samples based on their relative abundance. But the resultant files dont have the relative abundance calculated so how do I calculate the relative abundance.

Thanks

[sumah.1si21bt017]

Hi, I also have a question related to EukDetect. I’m particularly interested in how well it performs for detecting fungal species - is it generally considered efficient/accurate for that? Can it also be reliably used with shotgun metagenomic datasets?

In my case, I’m working on soil metagenomes where my focus is on both prokaryotes and eukaryotes. I came across the paper on EukDetect and also saw your post here, which made me curious.

Also, I’m wondering how you figured out the best way to calculate relative abundance from the output tables, since the tool doesn’t provide that directly. Did you normalize the read counts (e.g., dividing by total mapped reads per sample) or use another approach?

Thanks in advance for any insights!