Error with DADA2 with sequences of different runs.

User Support
1

Hello

I have 199 paired sequences with 4 different runs, I already have the PairedEndreads document of these sequences, but when I run the DADA2 gives me the next error. Previously, I had run-by-run analysis files, but they were with the 2022 version of qiime2. I wanted to switch to the 2024 and analyze everything together and avoid the merged of each file.

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2

Hello!

I guess it worked for you when you ran them separately. That means that with the combined dataset, your machine is running out of RAM.

Still, denoising each run is preferable:

  • You can save some RAM, so your machine can handle each run separately
  • DADA2 developers recommend denoising each run separately (with the same settings) to avoid biases introduced by different runs (related to the error model).

Best,

3

Previously analyzed run by run was united at the end, that is the best option?

4

Yes, that is the best option (but all the settings/steps before merging, such as cutadapt and dada2, should be identical).