Request for help with Barcode or Metafile

[Azospirillum871 (Elizabeth)]

Hi, I am new to Qiime2. I do not know how to create a barcode.fastq.gz file or a metadata file. I just got some paired-end sequences that my advisor gave me after we ran the Miseq together. Just the two reads per well no other files. I emailed my advisor about the barcode.fastq.gz file and told me "they are the indexes". I do have an excel sheet that I uploaded to the Miseq, I used two indexes per well (i.e N701-C TAAGGCGA S513-C TCGACTAG). I hope I am providing the right information for my question. Any help would be appreciated.

[llenzi (Luca)]

Hi @Azospirillum871,

I think your best bet is to follow the following tutorial:

Importing and Demultiplexing Sequence Data Quick Reference

The following is a “pocket guide” to determining the appropriate methods for importing and demultiplexing FASTA/FASTQ sequences (primarily from marker-gene sequencing experiments). Many samples are often “multiplexed” (pooled and sequenced together) on a single sequencing run. So the first step to analyzing these data is to demultiplex the data. Often, demultiplexing is performed automatically by sequencing centers/services and users. How can you tell if you have demultiplexed data? If you have …

From what you describe, you should have dual-barcode index, so you can import the fastq files you have and then demultiplex them using cutadapt, the command are summarised here:

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,…

(but is referring to an old version of QIIME2 so it may need some tweaking ...)

Hope it helps
Luca