How to prepare the barcodes.fastq.file

[angelrica_kuan]

Hi, I am new user. I obtained three files from NGS company as below:

1. MS18201-pool_R1_001.fastq.gz\
2. MS18201-pool_R2_001.fastq.gz\
3. Dual barcode sequences which are in excel file

My question is how to create a barcode. fastq. file?

Thanks for replying.

Angelrica

[Nicholas_Bokulich]

Welcome to the forum @angelrica_kuan!

I recommend discussing with the NGS company to figure out where your barcodes are located. I suspect they may be in-line in the forward and reverse sequences, in which case you can follow this tutorial to import and demux:

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,…

And note that qiime cutadapt demux-paired now supports dual-index barcodes (see the --help documentation for details).

Good luck!