Predict Functional potential microbial communities - phyloseq Silva

Question

[ymj]

Hi,

Does anyone have good tutorials/resources on how to predict the metabolic potential from microbiome data. I have preprocessed using DADA2, resulting in a phyloseq object. I assigned taxonomy with SILVA database. I found this Tax4fun package in R implemented in themetagenomics package, but this does not seem to work.

Thanks!

[antonioggsousa]

Hi,

I never used the Tax4fun package, but what was the error/problem that you obtained with that package?

Other option might be PICRUSt (see the link: https://github.com/picrust/picrust2) among others.

António

[ymj]

I installed everything successfully. I have tested reference data, built the dependencies, and added the bin to PATH. (according to : https://github.com/bwemheu/Tax4Fun2)

When trying to run with the test data using the command: runRefBlast(path_to_otus = "~/Thesis_Data/seqs/seqs.fasta", path_to_reference_data = PATH, path_to_temp_folder = "~/Thesis_Data/seqs/REF99NR", database_mode = "Ref99NR", use_force = T, num_threads = 4) I get this: Copy and generate database Reference blast started Error in if (file.size(path_to_blast_file) == 0) stop("Blast file empty!") : missing value where TRUE/FALSE needed

[antonioggsousa]

Did you check if your problem was related to this github issue: https://github.com/bwemheu/Tax4Fun2/issues/10

Which version do you have?

António

[ymj]

No, it was the correct vesion that I installed. actually, it was a very minor path problem .. thanks anyway !