Alpha and beta diversity analysis without sample-metadata.tsv

Hi
I am trying to check diversity of my Miseq data which is pared end(forward and reverse).

Since I followed ‘Fastq manifest’ formats, There is no ‘sample-metadata.tsv’ file.

“Fastq manifest” formats

qiime tools import
–type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path pe-33-manifest
–output-path demux.qza
–input-format PairedEndFastqManifestPhred33V2

In * “Atacama soil microbiome” tutorial, there is no step for alpha and beta diversity.
So I just tried qiime diversity core-metrics-phylogenetic without --m-metadata-file parameters

qiime diversity core-metrics-phylogenetic
–i-phylogeny rooted-tree.qza
–i-table table.qza
–p-sampling-depth 1000
–output-dir core-metrics-results

But it didn’t work with this error.

(1/1) Missing option “–m-metadata-file”.

Which file should I put for “–m-metadata-file”?

Hi! You should provide a metadata file with all samples names, treatments and whatever parameters of your samples according to which you want to analyze your data. In the tutorials section you can find nice explanations about it
https://docs.qiime2.org/2019.4/tutorials/metadata/
Good luck!

2 Likes

It works. Thanks a lot!

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