How to collapse Taxa bar plot in qiime version 2019.10?

[ilhem (sa)]

Hi, everyone

I am completely new to QIIME 2 so I apologize if this question has an obvious answer,I m doing the taxonomy analysis with qiime2 version 2019.10,
The taxa bar plots represents all the samples (24), but the 24 samples actually are only 8 samples and its replicates.
And I want to collapse the total 12 samples that the plot shows in to the 8 different samples that actually exists.

I have tried with this command

qiime feature-table group

--i-table table.qza

--m-metadata-file metadata.tsv

--m-metadata-column ??????

--p-axis sample

--p-mode mean-ceiling

--o-grouped-table grouped-table.qza

But I don’t know what to put in –m-metadata-column

Here I upload the metadata file and the sample that I want to collect presented in the red circle

[colinbrislawn (Colin J Brislawn)]

Good morning @ilhem,

Welcome to the Qiime 2 forums!

I think you are on the right track. qiime feature-table group is the perfect plugin to merge technical replicates.

@ilhem

But I don’t know what to put in –m-metadata-column

In order to get the grouping you showed in red, I would make a new metadata column, maybe called sample-id-no-rep

sample-id	sample-id-no-rep
sample5	sample5
sample51	sample5
sample52	sample5
sample6	sample6
sample61	sample6
sample62	sample6
...	...
sample163	sample16

This new column just just the same as sample-id, but now it no longer includes the replicate suffix. Once you pass this into the --m-metadata-column, samples with the same id prefix will be merged.

Let me know if that works OK for you!

Colin
P.S. Are these sequencing replicates or biological replicates? I like to keep my biological replicates separate because it lets me assess variation, but this choice is up to you.

[ilhem (sa)]

Hi
thank you for your reply
I have made new metadata

with the instruction that you give me and I run the following command and I receive the grouped-sample-no-rep-table.qza

qiime feature-table group

--i-table table.qza

--m-metadata-file metadatanorep

--m-metadata-column sample-id-no-rep

--p-axis sample

--p-mode mean-ceiling

--o-grouped-table grouped-sample-no-rep-table.qza

But when I try to summarize the table with the following command i get this error error-1|690x388

[quote="colinbrislawn, post:2, topic:14874"]
P.S. Are these sequencing replicates or biological replicates? I like to keep my biological replicates separate because it lets me assess variation, but this choice is up to you.
[/quote]they are biological replicate from each sample ,yes i will keep them seperate but just to check

[colinbrislawn (Colin J Brislawn)]

Looks like your table was groups successfully!

When you group a table, the grouping values become the new sample IDs, so the old metadata does not match. To fix this:

@jairideout

you’ll need to manually create a new metadata file that has new sample IDs corresponding to the group names in the metadata column you grouped by. The new “grouped” metadata file and feature table can then be used for downstream analyses.

---

@ilhem

they are biological replicate from each sample, yes i will keep them separate but just to check

Nice!

Let us know if you have any more questions, or feel free to open up a new thread!
Colin

[ilhem (sa)]

Thanks, it was the solution