Importing samples

I have a bunch of samples, where barcodes and primers have been removed, and the paired-end reads have already been merged. Each sample folder looks like this:


I tried to use qiime tools import to import these files but I get error messages on all of them. I am unsure of which type and the input_format to use. Can anyone help me? Thanks!

Hello @jboganes,

Check out the docs on the fastq manifest format, which could be a good way to import those joined reads as if they were single-end Illumina.

Let us know what you try and what errors you see, and we can help you get this working!



If you can get a copy of the raw data before processing, that would better match the examples on the website and would give you more control of how to process your data. If you don't have the raw data we can still make progress, but raw data is best!

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