A question about barcode removing

Hi everyone! I have 40 forward and 40 reverse fastq.gz files from 40 samples. Then I found that every file seems to have barcode and primer.

These files seems to be demultiplexed, so I can't import them use MultiplexedPairedEndBarcodeInSequence. Then I can't use demux-pair to remove these barcodes.

How can I remove the barcode?


I would import it to Qiime2 as demultiplexed reads and remove primers with cutadapt. Then check if barcodes were removed as well (sequences preceeding primers should be removed with the primer).

Thank you for your reply!
However, when I import it to qiime2 as demultiplexed reads and use cutadapt as follow:
time qiime cutadapt demux-paired \

--i-seqs paired-end-demux.qza
--m-forward-barcodes-file barcode-metadata.tsv
--m-forward-barcodes-column forward-barcodes
--m-reverse-barcodes-file barcode-metadata.tsv
--m-reverse-barcodes-column reverse-barcodes
--o-per-sample-sequences per_sample_sequences.qza
--o-untrimmed-sequences untrimmed_sequences.qza
Then I get the error:

I don't know how to solve this problem.

It is a misunderstanding - I suggested you proceed with biological primer removal with cutadapt, not demultiplexing with cutadapt. Did you try it?

Sorry for my misunderstanding. I just know how to remove primer by cutadapt, but I don't know how to use it to remove barcode of every sample. Can you tell me how to do it?

I guess it will be the same command you already know.

--p-front-f TEXT...     Sequence of an adapter ligated to the 5' end. The
    List[Str]             adapter and any preceding bases are trimmed. Partial
                          matches at the 5' end are allowed. If a `^`
                          character is prepended, the adapter is only found if
                          it is at the beginning of the read. Search in
                          forward read.                        

If barcodes are preceding your biological promers they should be removed with primers.

I would use --p-discard-untrimmed parameter enabled and then check if barcodes were removed with primers.

Thank you so much! I succeeded.

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