importing 4 initial read files (I1, I2, R1, R2) in Qiime2 2022.2

Hello everyone,

I am pretty new here and a novice in using Qiime. I have tried reading similar discussing but have not found a solution to my issue.

I have received my sequence from the sequencing company in formats I1, I2, R1, and R2, representing the barcodes and reads respectively. The sequence is demultiplexed. Below are the sequences


Q1: Does anyone has any idea what the first two fastq files represent.
Q2: How do I import this qiime2 for analysis.

Good morning Jerry,

Welcome to the forums! :qiime2:

I'll start with your last question:

Because your dual-indexed Illumina reads are already split up by sample, you can use the Fastq manifest format. This does not require those i1.fastq.gz or I1.fastq.gz files at all!

Now to the tricky question...

I'm not sure! Often i1 and i2 stand for 'Index 1' and 'Index 2', with these being the barcodes that label the sample they come from. But that would give you 4 files per sample (i1, i2, R1, R2) and not the 6 you see here. :thinking:

Could you post the first few lines of each of these samples? Maybe using a command like this:

gzip -dc M06648_0254_1_i1.fastq.gz | head -n 8
gzip -dc M06648_0254.001.FLD_ill_001_i7---IDT_i5_1.6NF1_NF1_I1.fastq.gz | head -n 8
gzip -dc MI.M06648_0254.001.FLD_ill_001_i7---IDT_i5_1.6NF1_NF1_R1.fastq.gz | head -n 8

... Or don't worry about it and use the paired-end Fastq manifest format!

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