Working with FASTA data in qiime2

Hi all, I am working with samples that are in FASTA format, I imported as indicated in the tutorial "Clustering sequences into OTUs using q2-vsearch" and everything fine, I could also do a taxonomic analysis and a tree and fine, but my doubt is the following: If I have 2 FASTA reads per sample, one forward and one reverse, how can I work as paired format in qiime2 with FASTA data?


Hello Karina,

Are you talking about this tutorial?

In that example, they have 1 fasta for their whole project, because they already took their fastq files through pairing and denoising.

You can't. But if you have a pair of fastQ files per sample, you can use vsearch for merging as shown here or dada2 for merging and denoisging as shown here.

Do you have the original fastq data or just the fasta files after they have been converted from the fastq format?

I only received FASTA files from the sequencing service, could I perhaps transfer them to fastq? :frowning:

Unfortunately no...

FASTQ has nucleotides and quality scores.
FASTA only has nucleotides (no quality scores).

Those quality scores are what makes fastq useful, and those have already been removed from your files. :crying_cat_face:

But your sequencing service should have your raw data, including the full fastq files! Ask them to send the original fastq files to you so you can do the processing yourself in Qiime! :sunglasses: :qiime2:

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