Problems with fastq files paired end without barcode file

Hello community I need your help,

I’m starting to work with qiime and I have two fastq files coming from MiSeq parsing end, no barcode file. What are the steps to be able to transform it to qza and follow the analysis.
Thank you very much for your help.


Hi @RAVargasC,

I am guessing that you mean you don’t have a separate barcodes.fastq file, but do have the BarcodeSequence used inside your mapping file-right? If so, that is usually how I receive my data and barcodes are located at the beginning of my R1 and R2 fastq files. I use 12 bp golay barcodes when sequencing and these can easily be extracted and then you can follow the qiime 2 tutorial.

  1. using qiime1
  2. Import data using qiime2 .
    3.Follow Moving Pictures Tutorial to demultiplex, denoise, ect…

Dear Torres thanks

I understand point 1 and point 3 in the post above mention

I do not understand point 2. Import data using Qiime.
I have data in my laptop drive. Tutorial only guide how to get data from web
wget, curl or url.

Hi @drmusk! The tutorials start with downloading tutorial data as an example (not everyone following the tutorials has their own data to follow along with!) — since you already have your data locally on your computer you can start with importing the results from Step 1 ( from above.

Just for reference, we have an open issue to add support for importing this type of multiplexed sequence data, where the barcodes are contained within the sequences. We’ll follow up here when it’s available in a QIIME 2 release!


An off-topic reply has been merged into an existing topic: Qiime dada2 denoise-paired end sequences

Please keep replies on-topic in the future.

Thanks for your answer, is there any way to get the barcodes in QIIME2 or do I have to install QUIIME1 to do it?

There is not at this time, so you’ll have to use from a QIIME 1 installation to perform this.

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This is now possible with q2-cutadapt! I think this functionality first became available in 2017.12, but you should check out 2018.2 which was just released!