ASVs relabeled OTUs when merging samples in shared table


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,” . 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

merge.groups is likely changing the label without changing anything else. I suspect what you’re seeing is really cosmetic. Do you have the same number of ASVs across all samples before and after running the command?


Yes, the number of ASVs before the merge seem to match the number of “OTUs” after the merge.

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