Hi,
I am trying to merge the sequences for 2 “before” and 2 “during” samples in my shared table. I am looking to analyze the data at the ASV level first, and thus my shared table “final.asv.shared” is as ASVs.
My problem arose when I went to combine my 2 “before” and 2 “during” samples with this code “merge.groups(shared=final.asv.shared, design=agrouptype.design)” . The output was a file called “final.asv.merge.shared”. It successfully merged the desired samples, but it suddenly started calling my ASVs OTUs.
To investigate if it was a labeling issue or if it had converted my ASVs to OTUs, I made relative abundance table for each shared table (the merged and non-merged). Notably, there are the same number of ASVs as “OTUs”. I then went to a sample that wasn’t combined with another sample (because it didn’t have two “before” samples), and I compared the abundances for each ASV in the non-merged file against the “OTU” in the merged file because they should be the same. They seemed to line up. This leads me to believe that it is a just a labeling issue, but I wanted to make sure that I didn’t accidentally switch to OTUs.
Any information on this issue or suggestions for double checking my data would be greatly appreciated!
Thank you