Diversity analysis needs metadata file for Casava 1.8 paired-end

Hello,
I am going through the Alpha and Beta Diversity analysis of a Casava 1.8 paired-end sample. I was able to get through the feature-table summary without providing a sample metadata file as the parameter was optional.
However, when i got to the diversity analysis the Sample-Metadata file is required. I thought i would not need a metadata file in the paired end samples, Is there a way around this for me to run the diversity? Or do i need to create a metadata file? If so, what should i include in it?
P.S: I am only running one sample at a time.

Hi @edy_shadows7,

You do not need to use a metadata file (i.e., with barcode information) for demultiplexing CASAVA 1.8 data, since those data are already demultiplexed.

However…

No, there is no other way. The point of pretty much any diversity analysis is to compare between samples, usually in the context of some metadata (where did that sample come from? How were two different groups of samples treated?). So metadata files are required.

Though if you really do only want to analyze one sample at a time, you could just use qiime diversity alpha directly to calculate alpha diversity on your one sample, without needing metadata.

Since you are running one sample at a time I understand why metadata would not make a difference. But running diversity analyses on a single sample also would not give a useful output — I suppose the alpha diversity data would be meaningful, but beta diversity would not.

I obviously don’t know the specifics of your analysis so apologize for the potentially naive comment — but it would probably make more sense to run the core diversity analyses once you have multiple samples merged together (with metadata on each). At least the core analyses, which include beta diversity analyses (which calculate between-sample dissimilarity).

You can see this example for what you might put in a metadata file used for diversity analyses: type of sample, sampling site/subject, sampling time, treatment group, sample pH, phase of the moon, zodiac sign, etc.

I hope that helps clear things up! Let me know if you have any more questions.

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