merging or grouping replicate data

Hi, I have a question about merging or grouping my replicate data sequences. I have processed my sequences separately but I would also like to combine them based upon sampling method.

For example, sample methods trialled: milling and blending of which I have 3 biological reps each with 3 technical reps. I would like to combine the technical reps within each biological rep as well as combining the biological replicates so that I can compare milling vs blending. I have labelled the samples as BT1.1, BT1.2 ...... BT2.1, BT2.2.... etc

I have tried the group feature table commands as per Best way to merge or group runs/samples but it seems to have only changed the original sample names to the replicate name e.g. SF### to BT1.1 etc, which I don't believe this is what I actually wanted. I am a bit confused as to if I have assessed it to early and need to follow through with the merge-seqs or merge-taxa commands but from reading about them they don't seem to the be commands that I need.

Is it possible to combine my technical and biological replicates in qiime?

I am using qiime 2021.4 on command line.



You need to use the same plugin you already tried to group replicates.
Your metadata file was probably not organized to group it.

It should be:

SampleID   Group
S1.1       S1
S1.2       S1
S1.3       S1
S2.1       S2
S2.2       S2
S2.3       S2

And after it should have samples, named S1 and S2 (names just for example)

Awesome, thank you so much, I have fixed it now and it has worked!

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