Hello, I see that the question I asked on the forum was answered by crusher083. However, I attempted without success to implement the solution. I thought I would ask you since I used the script from your prior posts. I exported the phyloseq object using the following script:-
Export taxonomy table as "tax.txt"
I used this step to export tax_table
tax_cols <- colnames(tax)
tax$taxonomy<-do.call(paste, c(tax[tax_cols], sep=";"))
for(co in tax_cols) tax[co]<-NULL
write.table(tax, "tax.txt", quote=FALSE, col.names=FALSE, sep="\t")
Export feature/OTU table
As a biom file
#if taxa_are_rows=TRUE use the following step
When I am trying to summarize the feature table, I'm still getting the "ValueError: The following IDs don't appear in the metadata" (log file attached). I have taken into account the answer from crusher083 (the sequences are rows and sample-ids columns). I could not process my data further. I included OTU, taxonomy and sample-metadata screenshots (from qiime2view). Can you help me in this respect, please?
PS biom is imported into qiime2 as follows
qiime tools import
Thanks in advance for your help.