Incorporating metadata when using manifests

[atgustin (andrew gustin)]

Hello!

I'm new to using Qiime2 and am working through my first project. My import step involved a manifest, as I already have demultiplexed fastqs:

qiime tools import --type SampleData[PairedEndSequencesWithQuality]
--input-path wihs_cvl_16s_manifest
--output-path demux.qza
--source-format PairedEndFastqManifestPhred33

This works without a problem. But I notice that I'm then skipping the demultiplexing step that incorporates my metadata file.

At a later point when tabulating meta data like this:

qiime metadata tabulate \

--m-input-file demux-filter-stats.qza
--o-visualization demux-filter-stats.qzv

i get an error like this:

There was an issue with viewing the artifact demux-filter-stats.qza as metadata:

Non-string Metadata index values detected. There may be more errors present in this metadata. Sample/feature metadata files can be validated using Keemei: http://keemei.qiime.org

I used Keemi to make sure the format of my .tsv metadata looked good and it gave me a green light.

I'm now wondering if the error is due to a lack of metadata incorporation - due to the demultiplexing that I skipped.

Your thoughts are much appreciated!

Andrew

[jairideout (Jai Ram Rideout)]

Hi @atgustin!

@atgustin

This works without a problem. But I notice that I’m then skipping the demultiplexing step that incorporates my metadata file.

Since your data are already demultiplexed, the demultiplexing step isn't necessary. When demultiplexing, the metadata file is used to look up the barcode sequence associated with each sample, but in your case the barcodes have already been removed and your sequences have been split into per-sample FASTQ files.

@atgustin

At a later point when tabulating meta data like this:

qiime metadata tabulate \

–m-input-file demux-filter-stats.qza

–o-visualization demux-filter-stats.qzv

i get an error like this:

There was an issue with viewing the artifact demux-filter-stats.qza as metadata:

Can you provide the wihs_cvl_16s_manifest file you used to import your FASTQ files? My hunch is that you have a sample ID called NA or something, which doesn't work with current QIIME 2 releases (that issue will be fixed in the upcoming 2018.2 release; we'll follow up here when that happens). Thanks!

[atgustin (andrew gustin)]

So I discovered that the metadata tabulation step that I was worried about isn't exaclt consequential - in the sense that it doesn't contribute to downstream analysis. I realized -after much qiime2 forum reading - that metadata is called for by each script independently. As a result of reading that, I was able to incorporate it at a later step - entirely skipping the metadata tabulate step.

I appreciate this forum a great deal - in the future i'll do a better job of patiently looking for my answer before posting a "new" question. Thanks!

Andrew

[jairideout (Jai Ram Rideout)]

In the QIIME 2 2018.2 release, Metadata now supports IDs and column names that are NA; this name will no longer be interpreted as missing data, which I think was the source of the original error reported in this topic.

There are a number of other changes to QIIME 2 Metadata in the 2018.2 release. See this forum announcement for details on what changed, as well as the updated Metadata tutorial.