How can I export each step of fastq OR fasta (filtered/denoised/merged/non-chimeric) in dada2

Hi All,

I want to know how I can export each step of fastq OR fasta (filtered/denoised/merged/non-chimeric) in dada2.

I know rep-seq fasta is exported by following command

qiime tools export --input-path rep-seqs.qza --output-path rep-seqs

Can QIIME2 or dada2 export all fasta/fastq files (filtered/denoised/merged/non-chimeric) ind dada2 ?


No, the output files from q2-dada2 can only be exported in fasta format, the quality scores are not preserved at that point.

No. You must run standalone dada2 in R if you want to run these steps and examine the results independently.

Good luck!

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