merging or grouping replicate data

[JessG]

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.

Thanks

Jess

[timanix (Timur Yergaliyev)]

Hi!
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)

[JessG]

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