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
sampleAB CTCTAGAG GATCGTGT
I load the sequences with
qiime tools import \
--type MultiplexedPairedEndBarcodeInSequence \
--input-path run1_mp \
How to integrate the tab-separated barcode file ? Are the I1 and I2 files necessary ?
Welcome to the forums!
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!
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 extract_barcodes.py
This worked out, now I have forward.fastq, reverse.fastq and barcodes.py
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