Hello, I am running into an error stating that my samples have duplicate barcodes. I have 3 illumina datasets for one project and the same barcodes were used for some of the samples. Before running any commands I concatenated the fastq files. I am trying to create a .biom file using this workflow https://github.com/LangilleLab/microbiome_helper/wiki/Amplicon-SOP-v2-(qiime2-2018.8)
Is there a particular point i can reach in this qiime 2 pipeline for each dataset and then compile the data so that it will give a usable .biom file or will the duplicate barcodes always be an issue? Thanks
Therein lies the problem. You will need to keep these runs separate for demultiplexing and for denoising. After that, you can merge your feature tables and sequences. See this tutorial for an example of merging the data after denoising, though that tutorial example shows data that have already been demultiplexed.
The barcodes are only an issue for demultiplexing. After that, you can forget about them.
However, we still wait to merge until after denoising because dada2 (if that's the denoising method you use) needs to build its error models off of individual runs.