how can I export a FASTA file from QIIME 2?

Hi. Users

I need Qiime2 data converted to fasta file for Picrust2 work.

If you use the following command, only the biom file will be extracted. Please let me know how to solve this problem.

Command :
qiime tools export --input-path denoise-table-filtered.qza --output-path ./export

Output : feature-table.biom

Hi @JHLee1,
You will want to use the same command but export your rep-seqs file that you got from dada2 and not your feature-table!
Hope that helps!

thank youuu, cherman2 !

When rep-seqs.qza is used as input, it is output as a fasta file. However, I would like to convert the final qza file (ex: taxa filtering) into a fasta file to use for downstream analysis. Is there no way?

HI @JHLee1,

It seems like you want to filter your sequences based on the content of contained within the feature-table. You can do that using the command:

qiime feature-table filter-seqs \
    --i-table   denoise-table-filtered.qza  \
    --i-data   rep-seqs.qza \
    --o-filtered-data   rep-seqs-filtered.qza

The above command will generate a new sequence file containing only the sequences found within the table. Then you can export that file to fasta format.

1 Like

Hi. SoilRotifer

thank you. I guess my understanding of Qiime was low.

Problem solved . !

Thank you !


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