Metadata file while combining multiple runs

[macrobiome (T)]

Hi, I am new to QIIME2 and currently using v2023.2 in a conda environment. I am doing 16S analysis and planning to combine samples from two different runs to increase my sample size (Examples: Samples 1-5 are on run 1 and samples 6-10 are on run 2).

I have already denoised the two runs separately based on dada2. I am referring to the Fecal Microbiota Transplant Study for combining the two runs. I have three questions:

1. While using the feature-table summarize command (below), we need to enter the sample metadata. Do I need to create a new metadata file combining the two runs?

2. If I need to choose to analyze only certain samples for a given analysis. Let's say samples 3 and 5 from run 1 and samples 7 and 8 from run 2. What is the best way to do that? Should I just edit the metadata file and remove everything except those samples?

Thank you and appreciate everyone's help in my QIIME2 learning thus far!

[timanix (Timur Yergaliyev)]

Hello!

@macrobiome

While using the feature-table summarize command (below), we need to enter the sample metadata. Do I need to create a new metadata file combining the two runs?

If you are working with already merged table, then yes.

@macrobiome

If I need to choose to analyze only certain samples for a given analysis. Let's say samples 3 and 5 from run 1 and samples 7 and 8 from run 2. What is the best way to do that? Should I just edit the metadata file and remove everything except those samples?

You can create new feature table by filtering old one to remove undesired samples by IDs or metadata.

[macrobiome (T)]

Thank you @timanix !

If you are working with already merged table, then yes.

I used the below command:

qiime feature-table merge
--i-tables table-1.qza
--i-tables table-2.qza
--o-merged-table table.qza

qiime feature-table merge-seqs
--i-data rep-seqs-1.qza
--i-data rep-seqs-2.qza
--o-merged-data rep-seqs.qza

If I essentially merge the two original metadata files, would that work?

You can create new feature table by filtering old one to remove undesired samples by IDs or metadata.

Would you be able to elaborate on this? Can I just remove certain samples from the metadata file in above step and go ahead with feature-table summarize? If not, what approach should I use?

Thank you again!

[timanix (Timur Yergaliyev)]

@macrobiome

I used the below command:

qiime feature-table merge
--i-tables table-1.qza
--i-tables table-2.qza
--o-merged-table table.qza

qiime feature-table merge-seqs
--i-data rep-seqs-1.qza
--i-data rep-seqs-2.qza
--o-merged-data rep-seqs.qza

Actually, I never tried to input data like this and not even sure if it will work. I just provide it using wildcard characters:

qiime feature-table merge
    --i-tables table-*.qza
    --o-merged-table merged-table.qza

qiime feature-table merge-seqs
    --i-data rep-seqs-*.qza
    --o-merged-data merged-rep-seqs.qza

@macrobiome

If I essentially merge the two original metadata files, would that work?

Yes, just concat or merge both metadata files to create a new one for merged tables.

@macrobiome

Would you be able to elaborate on this? Can I just remove certain samples from the metadata file in above step and go ahead with feature-table summarize? If not, what approach should I use?

Just remove undesired samples from metadata file and then filter feature table based on sample IDs in metadata file, like in this tutorial. BTW, check this tutorial, it contain a lot of examples how to filter your data based on features, samples, metadata columns and other parameters!