Diversity core metrics: metadata issue

[Nicholas_Bokulich]

Very glad you were able to work it out! Thank you for confirming!

[michal.lichvar]

Hello Nicholas

I would like to ask also about the necessity of metadata file in command qiime diversity core-metrics-phylogenetic.

My problem is … I don’t have metadata table, as my input to qiime is already demux (Illumina pair end sequences in fastq files).

I followed these tutorials

• to import pair end: https://docs.qiime2.org/2018.8/tutorials/importing/
• and to analyse: https://docs.qiime2.org/2018.8/tutorials/moving-pictures/#demultiplexing-sequences

In second tutorial, I remove option --m-metadata-file in all commands (DADA2 for example). I didn’t need it until diversity command. How can I follow?

Is there a command like:
qiime metadata
–i-input-file paired-end-demux.qza
–o-output-file metadata.tsv
?

Thanks in advance

Michal Lichvar

[Nicholas_Bokulich]

@michal.lichvar

I would like to ask also about the necessity of metadata file in command qiime diversity core-metrics-phylogenetic .

This is answered above:

Diversity core metrics: metadata issue

Mapping files are essential to the core-metrics pipelines, because these pipelines actually perform a series of commands that do use metadata, e.g., for statistical comparisons. If you only want measures of alpha diversity (e.g., richness) for each sample, and do not want to produce PCoA plots or any other information, then you can run those commands individually instead of using the core-metrics pipeline. You can use qiime diversity alpha to calculate alpha diversity (and you should really u…

@michal.lichvar

My problem is … I don’t have metadata table, as my input to qiime is already demux (Illumina pair end sequences in fastq files).

Sample metadata is used in many different commands — yes, for demux, but also for other steps. Because sample metadata can contain all sorts of information about samples!

@michal.lichvar

In second tutorial, I remove option --m-metadata-file in all commands (DADA2 for example). I didn’t need it until diversity command. How can I follow?

You need to create your own metadata file from scratch. Check out the metadata files in the tutorials you are following to see some examples. Read here for a complete guide on formatting etc.

@michal.lichvar

Is there a command like:
qiime metadata
–i-input-file paired-end-demux.qza
–o-output-file metadata.tsv
?

No, because only you know what metadata are associated with your samples. Again, check out the tutorials to see examples of what you might put in a metadata file.

[michal.lichvar]

Hello

Thanks for pointing me toward metadata page, I had already found it, but I was worried of manually writing the metadata. And also that I need BarcodeSequence and LinkerPrimerSequence columns, as there were in tutotial examples … and obviosly I don’t have them, since I import demux data.

I solved it by downloading TSV file from visualization of stats-dada2.qzv and altering the columns.

Thank you

[Nicholas_Bokulich]

@michal.lichvar

I was worried of manually writing the metadata

Unfortunately, yes — we have yet to devise a method to automatically compile metadata.

@michal.lichvar

And also that I need BarcodeSequence and LinkerPrimerSequence columns

You do not need those columns.

The metadata format is completely flexible — columns are only used as needed, and there are (essentially) no requirements on what needs to be in there — the tutorial you've seen gives the few rules.