Features table (table.qza) for demultiplexed paired end R1 & R2 sequences

Hi everyone,

I'm a new QIIME2 user. I have a question about the visualization of the features table. All I got from the sequencer is demultiplexed R1 and R2 fastq file (sampleID_01_L001_R1_001.fastq.gz.
sampleID_01_L001_R2_001.fastq.gz). I did not get any metadata tsv file. I imported my data using cassava 1.8. Then I run dada2:

qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired-end.qza
--p-trunc-len-f 200
--p-trim-left-f 23
--p-trunc-len-r 200
--p-trim-left-r 20
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--o-denoising-stats stats.qza

This generated three artifacts:

Next, I tried to generate Features table:

qiime feature-table summarize
--i-table table.qza
--o-visualization table.qzv
--m-sample-metadata-file sample-metadata.tsv

In the last line of the code above, I need to have a metadata tsv file but I never got it from the sequencer. Can I run the Feature-table without the metadata and will there be any missing data if I don't have the metadata file? Every tutorial I saw has a metadata file and I thought I might be missing that file.

Thank you in advance and I appreciate your help!

Hi @Abdul,

The metadata doesn't usually come from the sequencer; I'm going to direct you to this post which talks about metadata. (Its not super well indexed and might have been hard to find.)



Hi @jwdebelius,

Thank you so much for the suggestion! The other post clarified a lot for me. In my understanding, I have to create the metadata for my data. Sorry again for the basic questions but how can I get the DNA barcodes from my samples. I did not receive a separate file for the barcodes from the sequencer instead I got demultiplexed R1 and R2 reads?

Thank you,


Hi @Abdul,

There are different ways to import your data into QIIME 2 and a lot of people find this step challenging, because there are so many different ways to import the data! There's a format that lets you import the demultiplexed data already. My favorite way to do this is the manifest format. It gives you the most control over the way your data gets imported.


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Thanks, @jwdebelius! This is awesome! I will try this.

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