I am helping a colleague with an Illumina dataset that was initially run in qiime1 (1.9.0). She has written up a paper (it was ready for submission) - but we just learned that the sequences were never denoised. They were taken through the qiime pipeline, just without the denoising step.
I was looking for advice on the simplest way to denoise this dataset.
Would you recommend 1) re-running the sequences through the entire qiime2 pipeline or 2) using deblur on its own and then re-integrating into qiime?
It is possible to denoise via deblur within qiime2, but bring the denoised data back into qiime1 (I ask this because I am familiar with the qiime pipeline but not qiime2)?
I will be in charge of the sequence analysis and I have been using dada2 and phyloseq to analyze sequences and am just on day1 of teaching myself qiime2. (I am familiar with qiime)
I appreciate any feedback - many thanks for your time