Just a general question about word choice for a paper

[lyisrae1]

Hello there,

This is another query that was not specifically answered in the FAQs.

But can you please help me with a word choice for my analysis. I am currently saying that "PICRUSt2 predicted ###### gene copies from the submitted sequences". However, my advisors are unsure on the word choice and just want to say "genes" or "total genes" since they feel that saying "gene copies" is not the most correct.

Also, does PICRUSt2 normalize the gene values for the KO unstratified output? Or does it normalize the sample sequences values before predicting the amount of genes for KO unstratified output?

I know this is a silly request, but can you please help us so we can finish writing up this paper?

Thank you,
lyisrae1

[R-Wright-1]

Hi there,

It is difficult to give solid advice here without knowing the context of what you are wanting to say. If you were looking at the number predicted per genome/ASV in your analysis, then the correct wording would be gene copies. However, I think saying the predicted gene content of your sample is X would probably be the most accurate.

The answer to your second question depends on which output you are looking at. I think you can understand this most clearly by looking at the KO_metagenome_out/pred_metagenome_contrib.tsv file. Here you can see a breakdown for each sample-function-taxon contribution, where you can see the abundance of the taxon in the sample, the relative abundance of the taxon in the sample, "genome_function_count" (the number of copies predicted to be in the genome of this ASV), and then columns corresponding to the abundance of that function contributed by the taxon (equal to the abundance/relative abundance if the genome_function_count is 1). You will then see that in KO_metagenome_out/pred_metagenome_unstrat.tsv, the abundances for each sample are simply the sum of the "taxon_function_abun" column for each sample. Hopefully this helps?

Best wishes,
Robyn