I am working on 16s Microbiome data and trying to get ASV from the paired sequence data.
Fortunately, I have an example set of data; that is,
for the data, somebody already made OTU by using QIIME1.
So, my goal has been replicating this result in terms of the number and variety of features by using QIIME2.
Once I end up with a satisfactory pipeline which provides very close replication, I am planning to use this approach to the rest of the data.
Thanks to the responses in this forum, I could get very close ASV to the target OTU by using DADA2 procedure and GG taxonomy.
It looks like just a usual ASV. (e.g., level 6 has OTU_6_forward_GG.tsv (47.1 KB))
The thing is that the result based on the example data shows another form of OTU which looks like in the following txt file. (part of the data
OTU.txt (78.9 KB))
I am curious about the relation between the first ASV form and the OTU form in the txt file.
In particular, I am not sure why several duplicated taxonomys are assigned to the same OTU IDs, resulting in the number of rows becomes a lot larger (I cut it at 500 but the original # of rows is 2443).
I am not sure if I am delivering my question in the correct way.
But, any clue or hint would be very helpful to me.
Thank you in advance for your time.