Import multiplexed data

Hi have read the manual about importing carefully (Importing data — QIIME 2 2023.2.0 documentation).
Still I am struggling to load my data with the correct format.

I have 5 files

And a tab separated file with columns for sample_ids and barcodes

I load the sequences with

qiime tools import \
  --type MultiplexedPairedEndBarcodeInSequence \
  --input-path run1_mp \
  --output-path multiplexed-seqs.qza

How to integrate the tab-separated barcode file ? Are the I1 and I2 files necessary ?

Hello Mike,

Welcome to the forums! :qiime2:

As you have correctly identified, your barcodes are in your files, so
makes sense to use.


The I1 and I2 are Index 1 and Index2 for your forward and reverse reads. I would expect the barcodes to be inside these files, so these are necessary and need to be included!

To do this, try the cutadapt plugin. (It's not listed on the main importing page because it's a plugin.)

Let us know how it goes!

Dear Colin,
thank you for the fast reply. Actually, the barcodes are not part of the read sequences.
I have two separate barcodes files I1 and I2. And R1 and R2 for the reads.

From this post (Importing multiplexed paired-end data with separated barcode sequence files - #11 by ebolyen). I found the suggestion to use the old script
This worked out, now I have forward.fastq, reverse.fastq and

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