I want to import multiplexed paired end reads but I have no barcodes.fastq.gz

[omomo]

Hi everyone!
I want to import multiplexed paired end reads data. I know the sequences of barcodes I used for different samples. But I don`t have barcodes.fastq.gz file.

Firstly, I tried import data with manifest by PairedEndFastqManifestPhred33V2. It worked but got the qza file with the type of SampleData[PairedEndSequencesWithQuality]'.

So it did`t work if next I do the cutadapt (it requires MultiplexedPairedEndBarcodeInSequence type).

So I`m confused that what kind of method should I use to import data? If there is a way to get the barcodes.fastq.gz since I have the sequence of each barcode.

[thermokarst]

Please see this community tutorial:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin, w…

You will need to make a few adjustments to the commands listed there to make it work with paired-end reads. If you get stuck please check in with us here - thanks!

[omomo]

Hi @thermokarst

Thanks for your reply!!

I`ll have a try.

Best,
omomo