Hello.
I am writing to inquire about obtaining intermediate files from DADA2, such as a set of filtered, denoised, and merged reads in fastq formats.
Is it possible to get these files in the QIIME2 pipeline after running DADA2?
I am using QIIME2 version qiime2-amplicon-2023.9 on Mac OS.
Thank you very much.
Hi @microbiome_25,
Can you paste here the command you are using?
In particular, what options are you using for the output? (all the output into a folder with the '--output-dir' option or you are specifying the output file names?)
If you are using the '--output-dir' option I believe you are obtaining everything you can from dada2, to be honest I never actually used that option. So if the intermediate files that you are looking for are not there, I do not think there is a way to get them with the current version of the q2-plug in.
If you need them, you may need to try dada2 native from R, using the R and dada2 package installed within the qiime2 conda environment, if you want to be sure you are using the same version.
However, if you would like to tell us more what are your aims, we may be can help you suggesting the best way!
Hope it help.
Luca
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