How to manage fastq files with qiime2 that are already merged demultiplexed and trimed?

(DIANA) #1

I am using qiime2 2018.11.
I got files .fastq (only this, 1 gile per sample) from a company that perform microbiota analysis for me. The company told me that the files are already demultiplexed, merged and trimed.
I succeeded to import my files in qiime2 after creating a manifest file.
So I obtained a .qza file and a qzv to see the interactive quality plot. So I have only a forward reads.
But I don’t know what to do next with this files. Should I performed a denoising but how I can do since I have only forward reads? Should I directly use the .qza file to do the taxonomic analysis?

(Nicholas Bokulich) #2

Excellent! So you are ready to proceed by following the steps in one of the tutorials, e.g., moving pictures. Since your data are already merged, you should not use dada2 for denoising — use deblur instead.

You should probably import as pre-joined reads following these steps. The rest of that tutorial page will tell you how to use deblur after importing your pre-joined (merged) reads.

You should perform denoising or OTU clustering. You will not be able to proceed to taxonomic analysis with out performing these steps (QIIME 2 will stop you!). The fact that your reads are already merged is not a problem for deblur!

Good luck!

(DIANA) #3

Its is working well now!