Why Do I have 4 fastq file for each sample and how can I import them and apply denoising process

[ptalebic (Pasha Talebi Charmchi)]

Hi,

I have fastq files generated using Illumina MiSeq. My samples are demultiplexed. After downloading these files I noticed that there are 4 fastq files per sample as shown below. I was wondering if they are from 4 sequencing run. If yes, How can I import them so I can apply denoising process on each.

This is a screenshot of my fastq files

Sorry I am new in this field and qiime as well.

[jwdebelius (Justine Debelius)]

Hi @ptalebic,

My go-to people on questions about sequencing runs is to ask your sequencing provider. Every single one I’ve worked with does things slightly differently. They can tell you about how the samples were sequenced or processed much more easily than we can. Once you know that, then we’re totally happy to help you get the sequences into QIIME 2 for denoising.

Best,
Justine

[ptalebic (Pasha Talebi Charmchi)]

Dear Justine

I have downloaded my data from European Nucleotide Archive using an accession number provided in the paper I read. Is there any other way I can find out how they were sequenced?

[jwdebelius (Justine Debelius)]

Hi @ptalebic,

That’s harder to say. Is there additional information in the upload that describes the relationship? I might still recommend contacting the corresponding author see if, for example, the samples were run in multiple parts. Often, ENA submission will include information about sequencing. The mod team has been wondering if there might be multiple lanes, and so perhaps reviewing some of that metadata might also help.

Best,
Justine