Importing fastq files into Qiime2

Hello there :slight_smile:

I was using Qiime2 once on the server and now I installed it on my computer using VM.
I have an issues with importing fastq files from the folder on my computer into Qiime2.
The folders on my computer are in this format:

I tried to follow tutorials and answers on this forum, but I'm a bit lost.
So, any help is very welcome!
Many thanks in advance! :blush:

Hello Milena,

Based on your screen, it looks like these files are on a Windows system. Your first step will be to set up a shared folder so that your Qiime VM can access these files.

There is a great tutorial on how to do this here: VirtualBox Shared Folders The instruction as the end are a little different for MacOS and Windows, but the start is exactly the same.

Let me know if you have any problems setting up the Shared Folder on the Qiime VM.


Hi @milena,

Thanks @colinbrislawn! That is definitely the first step. Once you have access to the files within your VM, you should be able to use this format to import. You might need to gzip your fastq files first (I’m not certain how Windows lists fastq.gz in their file browser). Let us know if it looks like that is the case. Otherwise, your filenames should be automatically understood by QIIME 2.

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