Thank you for your response! I figured out from my sequencing center that the data I received is demultiplexed and Casava 1.8 paired-end demultiplexed fastq. I imported it and unzipped them! When is the best time in analysis to remove barcodes? After denoising (can I use both dada2 and deblur?) before joining paired ends?
Thanks a ton!
You will definitely want to remove the before denoising, DADA2 cannot have any non-biological sequences in your samples. By import, did you run qiime tools import? You should not need to unzip the output .qza.
After that it sounds like your workflow is to remove non-biological sequences with q2-cutadapt, denoise with DADA2, and perform any filtering that you want(Deblur or quality-filter), and then assign taxonomy.
Hope that clears things up!
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